vignettes/query_download.Rmd
query_download.Rmd
eQTL_sig1 <- xQTLquery_eqtlSig("rs201327123")
eQTL_sig1 <- xQTLquery_eqtlSig("chr1_14677_G_A_b38")
# Query significant eQTL associations with a variant id in a specified tissue:
eQTL_sig1 <- xQTLquery_eqtlSig("chr1_14677_G_A_b38",
tissueSiteDetail="Skin - Sun Exposed (Lower leg)")
eQTL_sig1#> variantId snpId gencodeId geneSymbol
#> 1: chr1_14677_G_A_b38 rs201327123 ENSG00000241860.6 RP11-34P13.13
#> 2: chr1_14677_G_A_b38 rs201327123 ENSG00000228463.9 AP006222.2
#> 3: chr1_14677_G_A_b38 rs201327123 ENSG00000228327.3 RP11-206L10.2
#> tissueSiteDetail pValue nes datasetId
#> 1: Skin - Sun Exposed (Lower leg) 8.00361e-11 0.857182 gtex_v8
#> 2: Skin - Sun Exposed (Lower leg) 3.30591e-09 -0.746043 gtex_v8
#> 3: Skin - Sun Exposed (Lower leg) 1.23187e-15 0.688242 gtex_v8
varInfo <- xQTLquery_varPos(chrom="chr1", pos=c(1102708))
eQTL_sig2 <- xQTLquery_eqtlSig(variantName=varInfo$snpId)
head(eQTL_sig2)#> variantId snpId gencodeId geneSymbol
#> 1: chr1_1102708_G_C_b38 rs66622470 ENSG00000131591.17 C1orf159
#> 2: chr1_1102708_G_C_b38 rs66622470 ENSG00000131591.17 C1orf159
#> 3: chr1_1102708_G_C_b38 rs66622470 ENSG00000131591.17 C1orf159
#> 4: chr1_1102708_G_C_b38 rs66622470 ENSG00000131591.17 C1orf159
#> 5: chr1_1102708_G_C_b38 rs66622470 ENSG00000131591.17 C1orf159
#> 6: chr1_1102708_G_C_b38 rs66622470 ENSG00000131591.17 C1orf159
#> tissueSiteDetail pValue nes datasetId
#> 1: Brain - Amygdala 1.60336e-06 -0.459798 gtex_v8
#> 2: Brain - Anterior cingulate cortex (BA24) 8.66605e-07 -0.454671 gtex_v8
#> 3: Brain - Caudate (basal ganglia) 8.31578e-13 -0.472193 gtex_v8
#> 4: Brain - Cerebellar Hemisphere 2.37523e-06 -0.329395 gtex_v8
#> 5: Brain - Cerebellum 7.84906e-08 -0.392030 gtex_v8
#> 6: Brain - Cortex 9.13735e-13 -0.516023 gtex_v8
eQTL_sig3 <- xQTLquery_eqtlSig(genes="ATAD3B")
eQTL_sig3 <- xQTLquery_eqtlSig(genes=c("TP53", "SLC35E2B"), tissueSiteDetail= "Brain - Cerebellum")
eQTL_sig3 <- xQTLquery_eqtlSig(genes="ENSG00000141510.16")
head(eQTL_sig3)#> variantId snpId gencodeId geneSymbol
#> 1: chr17_7559785_G_A_b38 rs143094271 ENSG00000141510.16 TP53
#> 2: chr17_7668434_T_G_b38 rs78378222 ENSG00000141510.16 TP53
#> 3: chr17_7675353_C_T_b38 rs35850753 ENSG00000141510.16 TP53
#> 4: chr17_7668434_T_G_b38 rs78378222 ENSG00000141510.16 TP53
#> 5: chr17_7668434_T_G_b38 rs78378222 ENSG00000141510.16 TP53
#> 6: chr17_7441178_C_T_b38 rs4151125 ENSG00000141510.16 TP53
#> tissueSiteDetail pValue nes datasetId
#> 1: Adipose - Subcutaneous 1.00467e-05 -0.403825 gtex_v8
#> 2: Adipose - Subcutaneous 8.68606e-10 -0.765786 gtex_v8
#> 3: Adipose - Subcutaneous 1.34916e-05 -0.401123 gtex_v8
#> 4: Cells - Cultured fibroblasts 9.07463e-06 -0.473760 gtex_v8
#> 5: Esophagus - Mucosa 5.18785e-07 -0.729226 gtex_v8
#> 6: Kidney - Cortex 7.27802e-07 -0.541302 gtex_v8
eQTL_sig4 <- xQTLquery_eqtlSig(variantName="rs1641513", genes="TP53")
eQTL_sig4 <- xQTLquery_eqtlSig(variantName="chr1_1667948_A_G_b38",
genes="SLC35E2B", tissueSiteDetail="Kidney - Cortex")
eQTL_sig4#> variantId snpId gencodeId geneSymbol
#> 1: chr1_1667948_A_G_b38 rs368438548 ENSG00000189339.11 SLC35E2B
#> tissueSiteDetail pValue nes datasetId
#> 1: Kidney - Cortex 7.21369e-14 -1.05597 gtex_v8Multi-tissue eQTL metasoft results for a given gene and
variant can be also queried using xQTLquery_eqtl, the
results include: m-value (mValue), normalized effect size (nes), p-value
(pValue) and standard error (se).
# Query with a gene symbol:
eqtlMeta <- xQTLquery_eqtl(gene="TP53")
# Query with a variant-gene pair:
eqtlMeta <- xQTLquery_eqtl(variantName="rs1641513",gene="TP53")
head(eqtlMeta)#> variantId snpId gencodeId geneSymbol
#> 1: chr17_7650924_T_C_b38 rs1641513 ENSG00000141510.16 TP53
#> 2: chr17_7650924_T_C_b38 rs1641513 ENSG00000141510.16 TP53
#> 3: chr17_7650924_T_C_b38 rs1641513 ENSG00000141510.16 TP53
#> 4: chr17_7650924_T_C_b38 rs1641513 ENSG00000141510.16 TP53
#> 5: chr17_7650924_T_C_b38 rs1641513 ENSG00000141510.16 TP53
#> 6: chr17_7650924_T_C_b38 rs1641513 ENSG00000141510.16 TP53
#> tissueSiteDetail pValue nes se mValue
#> 1: Adipose - Subcutaneous 0.00992404 0.1065590 0.0411719 0.988
#> 2: Adipose - Visceral (Omentum) 0.02456600 0.0985826 0.0436840 0.953
#> 3: Adrenal Gland 0.49990900 0.0580124 0.0858289 0.729
#> 4: Artery - Aorta 0.84236100 -0.0113147 0.0568473 0.670
#> 5: Artery - Coronary 0.51525500 0.0624194 0.0957326 0.745
#> 6: Artery - Tibial 0.01521470 0.1224370 0.0502740 0.963
#> datasetId
#> 1: gtex_v8
#> 2: gtex_v8
#> 3: gtex_v8
#> 4: gtex_v8
#> 5: gtex_v8
#> 6: gtex_v8
sQTL_sig1 <- xQTLquery_sqtlSig(variantName="rs201327123")
sQTL_sig1 <- xQTLquery_sqtlSig(variantName="chr1_14677_G_A_b38", tissueSiteDetail="Whole Blood")
sQTL_sig1#> variantId snpId gencodeId geneSymbol
#> 1: chr1_14677_G_A_b38 rs201327123 ENSG00000227232.5 WASH7P
#> phenotypeId tissueSiteDetail pValue
#> 1: chr1:15947:16607:clu_40980:ENSG00000227232.5 Whole Blood 7.14888e-08
#> nes datasetId
#> 1: 0.756834 gtex_v8
sQTL_sig2 <- xQTLquery_sqtlSig(genes="ENSG00000141510.16", tissueSiteDetail="Lung" )
sQTL_sig2 <- xQTLquery_sqtlSig(genes=c("ATAD3B", "MLH1"))
sQTL_sig2#> variantId snpId gencodeId geneSymbol
#> 1: chr3_37136656_CAAAGA_C_b38 rs200076067 ENSG00000076242.14 MLH1
#> 2: chr3_37282912_C_T_b38 rs112128385 ENSG00000076242.14 MLH1
#> 3: chr1_1259424_T_C_b38 rs11804831 ENSG00000160072.19 ATAD3B
#> 4: chr1_1274256_A_G_b38 rs3737722 ENSG00000160072.19 ATAD3B
#> 5: chr1_1274972_A_G_b38 rs11260575 ENSG00000160072.19 ATAD3B
#> ---
#> 6330: chr1_1532105_T_C_b38 rs1987191 ENSG00000160072.19 ATAD3B
#> 6331: chr1_1533018_T_C_b38 rs6695186 ENSG00000160072.19 ATAD3B
#> 6332: chr1_1533095_G_A_b38 rs6677993 ENSG00000160072.19 ATAD3B
#> 6333: chr1_1533178_A_G_b38 rs6694773 ENSG00000160072.19 ATAD3B
#> 6334: chr1_1533253_C_T_b38 rs6690064 ENSG00000160072.19 ATAD3B
#> phenotypeId
#> 1: chr3:37040294:37047519:clu_44299:ENSG00000076242.14
#> 2: chr3:37040294:37047519:clu_44299:ENSG00000076242.14
#> 3: chr1:1487914:1489204:clu_52051:ENSG00000160072.19
#> 4: chr1:1487914:1489204:clu_52051:ENSG00000160072.19
#> 5: chr1:1487914:1489204:clu_52051:ENSG00000160072.19
#> ---
#> 6330: chr1:1487914:1489204:clu_41146:ENSG00000160072.19
#> 6331: chr1:1487914:1489204:clu_41146:ENSG00000160072.19
#> 6332: chr1:1487914:1489204:clu_41146:ENSG00000160072.19
#> 6333: chr1:1487914:1489204:clu_41146:ENSG00000160072.19
#> 6334: chr1:1487914:1489204:clu_41146:ENSG00000160072.19
#> tissueSiteDetail pValue nes datasetId
#> 1: Adipose - Subcutaneous 4.23971e-07 1.224370 gtex_v8
#> 2: Adipose - Subcutaneous 7.92886e-08 1.234820 gtex_v8
#> 3: Adipose - Subcutaneous 2.63274e-06 -0.334712 gtex_v8
#> 4: Adipose - Subcutaneous 1.92720e-06 -0.405750 gtex_v8
#> 5: Adipose - Subcutaneous 1.74607e-06 -0.389751 gtex_v8
#> ---
#> 6330: Whole Blood 3.35898e-07 -0.589917 gtex_v8
#> 6331: Whole Blood 4.09835e-06 -0.483704 gtex_v8
#> 6332: Whole Blood 2.61330e-07 -0.601543 gtex_v8
#> 6333: Whole Blood 5.63455e-07 -0.581156 gtex_v8
#> 6334: Whole Blood 3.35898e-07 -0.589917 gtex_v8
sQTL_sig3 <- xQTLquery_sqtlSig(variantName="rs201327123", genes=c("WASH7P","RP11-206L10.2"))
sQTL_sig3 <- xQTLquery_sqtlSig(variantName="chr17_7465085_A_G_b38", genes="TP53",
tissueSiteDetail="Lung")
sQTL_sig3#> variantId snpId gencodeId geneSymbol
#> 1: chr17_7465085_A_G_b38 rs546057177 ENSG00000141510.16 TP53
#> phenotypeId tissueSiteDetail
#> 1: chr17:7669690:7670609:clu_13833:ENSG00000141510.16 Lung
#> pValue nes datasetId
#> 1: 1.29439e-05 -0.566684 gtex_v8
eqtlAssos <- xQTLdownload_eqtlAllAsso(gene="MLH1", variantName = "rs13315355", study="")
eqtlAssos <- xQTLdownload_eqtlAllAsso("ATP11B", tissueLabel="Muscle - Skeletal")data_source="liLab" (only support GTEx
tissues)
eqtlAssos <- xQTLdownload_eqtlAllAsso("ATP11B", tissueLabel="Muscle - Skeletal", data_source = "liLab")
# gencode ID is recommended:
eqtlAssos <- xQTLdownload_eqtlAllAsso("ENSG00000058063.15", tissueLabel="Muscle - Skeletal", data_source = "liLab")
eqtlAssos <- xQTLdownload_eqtlAllAsso(variantName="rs11568818", study="")
eqtlAssos <- xQTLdownload_eqtlAllAsso(variantName="chr11_102530930_T_C_b38",
tissueLabel="Muscle - Skeletal", study="GTEx_V8")
eqtlAssos <- xQTLdownload_eqtlAllAsso(gene="MMP7",tissueLabel = "CD4+ T cell", study="")
eqtlAssos#> variantId snpId type maf beta chrom
#> 1: chr11_101531348_T_C_b38 rs4254048 SNP 0.3097830 0.0909405 11
#> 2: chr11_101531533_A_G_b38 rs11224820 SNP 0.1548910 0.0891349 11
#> 3: chr11_101532218_A_G_b38 rs145907949 SNP 0.0135870 -0.5316370 11
#> 4: chr11_101532331_A_G_b38 rs138388841 SNP 0.0135870 0.1777300 11
#> 5: chr11_101532593_G_A_b38 rs61916052 SNP 0.0108696 0.1754850 11
#> ---
#> 19131: chr11_103529577_C_A_b38 rs12365191 SNP 0.0674157 0.4218230 11
#> 19132: chr11_103529693_T_TTGTG_b38 rs147237734 INDEL 0.3595510 0.1532910 11
#> 19133: chr11_103529825_T_C_b38 rs34949425 SNP 0.2247190 -0.1864580 11
#> 19134: chr11_103530122_T_C_b38 rs4754958 SNP 0.3089890 0.7059100 11
#> 19135: chr11_103530486_C_G_b38 rs17380432 SNP 0.3314610 -0.1633750 11
#> pos ref alt se median_tpm pValue totalAlleles
#> 1: 101531348 T C 0.210025 5.637 0.6655640 368
#> 2: 101531533 A G 0.256792 5.637 0.7289380 368
#> 3: 101532218 A G 0.837931 5.637 0.5266310 368
#> 4: 101532331 A G 0.807995 5.637 0.8261630 368
#> 5: 101532593 G A 1.179750 5.637 0.8819290 368
#> ---
#> 19131: 103529577 C A 0.438372 0.000 0.3390160 178
#> 19132: 103529693 T TTGTG 0.242597 0.000 0.5293910 178
#> 19133: 103529825 T C 0.273032 0.000 0.4967640 178
#> 19134: 103530122 T C 0.282450 0.000 0.0146332 178
#> 19135: 103530486 C G 0.246976 0.000 0.5103180 178
#> allelCounts imputationR2 condition molecular_trait_id
#> 1: 114 0.94063 None ENSG00000137673
#> 2: 57 0.95629 None ENSG00000137673
#> 3: 5 0.94880 None ENSG00000137673
#> 4: 6 0.69826 None ENSG00000137673
#> 5: 4 0.73096 None ENSG00000137673
#> ---
#> 19131: 12 0.97970 CD4_T-cell_anti-CD3-CD28 ENSG00000137673
#> 19132: 63 0.87166 CD4_T-cell_anti-CD3-CD28 ENSG00000137673
#> 19133: 40 0.98203 CD4_T-cell_anti-CD3-CD28 ENSG00000137673
#> 19134: 55 0.98227 CD4_T-cell_anti-CD3-CD28 ENSG00000137673
#> 19135: 59 0.98326 CD4_T-cell_anti-CD3-CD28 ENSG00000137673
#> gene_id study_id tissue tissue_label
#> 1: ENSG00000137673 GENCORD CL_0000624 T cell
#> 2: ENSG00000137673 GENCORD CL_0000624 T cell
#> 3: ENSG00000137673 GENCORD CL_0000624 T cell
#> 4: ENSG00000137673 GENCORD CL_0000624 T cell
#> 5: ENSG00000137673 GENCORD CL_0000624 T cell
#> ---
#> 19131: ENSG00000137673 Schmiedel_2018 CL_0000624 CD4+ T cell
#> 19132: ENSG00000137673 Schmiedel_2018 CL_0000624 CD4+ T cell
#> 19133: ENSG00000137673 Schmiedel_2018 CL_0000624 CD4+ T cell
#> 19134: ENSG00000137673 Schmiedel_2018 CL_0000624 CD4+ T cell
#> 19135: ENSG00000137673 Schmiedel_2018 CL_0000624 CD4+ T cell
#> qtl_group geneSymbol gencodeId_GTEX_v8
#> 1: T-cell MMP7 ENSG00000137673.8
#> 2: T-cell MMP7 ENSG00000137673.8
#> 3: T-cell MMP7 ENSG00000137673.8
#> 4: T-cell MMP7 ENSG00000137673.8
#> 5: T-cell MMP7 ENSG00000137673.8
#> ---
#> 19131: CD4_T-cell_anti-CD3-CD28 MMP7 ENSG00000137673.8
#> 19132: CD4_T-cell_anti-CD3-CD28 MMP7 ENSG00000137673.8
#> 19133: CD4_T-cell_anti-CD3-CD28 MMP7 ENSG00000137673.8
#> 19134: CD4_T-cell_anti-CD3-CD28 MMP7 ENSG00000137673.8
#> 19135: CD4_T-cell_anti-CD3-CD28 MMP7 ENSG00000137673.8
sqtlAssos<-xQTLdownload_sqtlAllAsso(genes=c("MMP7","TP53"), geneType = "geneSymbol", tissue="Lung")
sqtlAssos#> rsid clu_name pValue beta se gencodeId
#> 1: rs4254048 clu_9701 0.4562150 0.05216700 0.0699585 ENSG00000137673.8
#> 2: rs11224820 clu_9701 0.0334606 -0.18979000 0.0889982 ENSG00000137673.8
#> 3: rs138388841 clu_9701 0.6221730 0.08717970 0.1768040 ENSG00000137673.8
#> 4: rs61916052 clu_9701 0.4701730 0.13079100 0.1809620 ENSG00000137673.8
#> 5: rs78752240 clu_9701 0.3274160 -0.33715300 0.3439250 ENSG00000137673.8
#> ---
#> 36276: rs59885278 clu_13833 0.2352270 0.22514800 0.1894450 ENSG00000141510.16
#> 36277: rs73251879 clu_13833 0.9783160 0.00368261 0.1354170 ENSG00000141510.16
#> 36278: rs58698225 clu_13833 0.9029850 0.00683635 0.0560565 ENSG00000141510.16
#> 36279: rs12935932 clu_13833 0.8615360 -0.01098430 0.0629434 ENSG00000141510.16
#> 36280: rs4346241 clu_13833 0.0140373 -0.16665600 0.0676048 ENSG00000141510.16
aqtlAssos <- xQTLdownload_xqtlAllAsso(genes=c("MMP7"), tissue="Lung")
aqtlAssos#> rsid maf pValue beta se
#> 1: rs2701977 0.5743146 0.0007479838 -2.100113e-01 0.06186416
#> 2: rs1711402 0.8896104 0.0012343600 -3.024068e-01 0.09300488
#> 3: rs1784450 0.8896104 0.0014384863 -2.965600e-01 0.09248070
#> 4: rs948138 0.5512266 0.0015553106 -1.948009e-01 0.06118752
#> 5: chr11_102631148_C_T_b38 0.5808081 0.0017118558 -1.949774e-01 0.06179620
#> ---
#> 4178: rs2846715 0.5389611 0.9964685792 2.647676e-04 0.05978774
#> 4179: rs2846342 0.5389611 0.9964685792 2.647676e-04 0.05978774
#> 4180: rs4254048 0.3145743 0.9993855679 5.160473e-05 0.06697517
#> 4181: rs7123862 0.6360347 0.9996407735 2.974098e-05 0.06602145
#> 4182: rs10895249 0.3831169 0.9999300442 5.476405e-06 0.06242669
#> mRNA gencodeId
#> 1: NM_002423.5 ENSG00000137673.8
#> 2: NM_002423.5 ENSG00000137673.8
#> 3: NM_002423.5 ENSG00000137673.8
#> 4: NM_002423.5 ENSG00000137673.8
#> 5: NM_002423.5 ENSG00000137673.8
#> ---
#> 4178: NM_002423.5 ENSG00000137673.8
#> 4179: NM_002423.5 ENSG00000137673.8
#> 4180: NM_002423.5 ENSG00000137673.8
#> 4181: NM_002423.5 ENSG00000137673.8
#> 4182: NM_002423.5 ENSG00000137673.8
mQTL_meta<- xQTLdownload_mqtlmeta("Prostate")
mQTL_dt <- xQTLdownload_mQTL(cpg_id="cg00000221", tissue_name="Prostate")
mQTL_dt#> variant_id gene maf pValue beta se
#> 1: chr17_48080661_G_A_b38 cg07625849 0.2238100 0.7905950 0.0295557 0.110913
#> 2: chr17_48080688_T_C_b38 cg07625849 0.2238100 0.0787432 0.2099310 0.117806
#> 3: chr17_48081171_T_C_b38 cg07625849 0.1380950 0.0706286 0.2153530 0.117448
#> 4: chr17_48081344_A_T_b38 cg07625849 0.0190476 0.6815340 -0.1598080 0.387928
#> 5: chr17_48081546_C_G_b38 cg07625849 0.2238100 0.0787432 0.2099310 0.117806
#> ---
#> 2774: chr17_49079069_C_G_b38 cg07625849 0.2238100 0.3348770 -0.1138980 0.117360
#> 2775: chr17_49079242_G_A_b38 cg07625849 0.0952381 0.1356170 0.2237770 0.148361
#> 2776: chr17_49079593_G_A_b38 cg07625849 0.0380952 0.3482250 -0.2615080 0.277058
#> 2777: chr17_49079687_A_T_b38 cg07625849 0.0142857 0.4095380 0.3410300 0.411232
#> 2778: chr17_49080066_G_A_b38 cg07625849 0.1809520 0.1526370 -0.1839900 0.127350
hqtlmeta <- xQTLdownload_hqtlmeta(histone_type="H3K4ME1", cell_type="T cell")
hQTL_dt <- xQTLdownload_hqtl(phenotype_id="10:10458128-10465096",
histone_type="H3K4ME1", cell_type="T cell")
hQTL_dt#> rsid gene maf pValue beta se
#> 1: rs950228 10:10458128:10465096 0.4850 0.3871 -0.12300 0.1422
#> 2: rs12783041 10:10458128:10465096 0.3850 0.4063 0.11590 0.1396
#> 3: rs7903944 10:10458128:10465096 0.4825 0.4623 -0.10580 0.1439
#> 4: rs10905556 10:10458128:10465096 0.4800 0.3548 -0.13040 0.1409
#> 5: rs34488055 10:10458128:10465096 0.1275 0.7625 -0.06456 0.2136
#> ---
#> 4209: rs72777637 10:10458128:10465096 0.0550 0.8334 0.06993 0.3325
#> 4210: rs2440112 10:10458128:10465096 0.7375 0.5641 -0.10610 0.1840
#> 4211: rs77085282 10:10458128:10465096 0.0525 0.5223 0.20470 0.3199
#> 4212: rs7068574 10:10458128:10465096 0.1900 0.8650 -0.03029 0.1782
#> 4213: rs2499927 10:10458128:10465096 0.0525 0.2223 0.42320 0.3468
#> variantId
#> 1: 10:9458147_A_G
#> 2: 10:9459295_T_C
#> 3: 10:9459626_C_T
#> 4: 10:9460058_C_T
#> 5: 10:9463102_A_G
#> ---
#> 4209: 10:11461313_T_C
#> 4210: 10:11462143_T_C
#> 4211: 10:11464056_T_C
#> 4212: 10:11464106_G_C
#> 4213: 10:11464602_T_AResztak2022biorxiv:
# Get details of sc-eQTL study:
study_info <- xQTLquery_scInfo()
sceQTL_dt <- xQTLdownload_sc(gene="TP53", cell_type = "B Cell", cell_state="-",
qtl_type="Cell-type-specific eQTL", study_name = "Resztak2022biorxiv")
sceQTL_dt#> beta cellType chromosome geneSymbol pValue pos
#> 1: -0.0120341 B Cell chr17 TP53 0.894893 7639177
#> 2: -0.0122527 B Cell chr17 TP53 0.892879 7639273
#> 3: -0.0866685 B Cell chr17 TP53 0.340513 7639553
#> 4: -0.0135121 B Cell chr17 TP53 0.881551 7639699
#> 5: -0.0181303 B Cell chr17 TP53 0.839595 7640154
#> ---
#> 260: -0.162146 B Cell chr17 TP53 0.0816707 7697870
#> 261: 0.13485 B Cell chr17 TP53 0.235491 7719119
#> 262: -0.121788 B Cell chr17 TP53 0.303225 7722187
#> 263: 0.070017 B Cell chr17 TP53 0.602875 7722656
#> 264: 0.18766 B Cell chr17 TP53 0.0818137 7724742
#> qtlType se snpId
#> 1: Cell-type-specific eQTL 0.0910877781405 rs2430948
#> 2: Cell-type-specific eQTL 0.0909884473621 rs1642795
#> 3: Cell-type-specific eQTL 0.0909282976755 rs1642796
#> 4: Cell-type-specific eQTL 0.0906832041021 rs1642797
#> 5: Cell-type-specific eQTL 0.0895714697899 rs12450254
#> ---
#> 260: Cell-type-specific eQTL 0.0931299007474 rs1393370347
#> 261: Cell-type-specific eQTL 0.113669645877 rs373872446
#> 262: Cell-type-specific eQTL 0.11829336382 rs1052202011
#> 263: Cell-type-specific eQTL 0.134578050437 rs8070743
#> 264: Cell-type-specific eQTL 0.107834576496 rs370880934
#> study variantId
#> 1: Resztak2022biorxiv_qtl rs2430948
#> 2: Resztak2022biorxiv_qtl rs1642795
#> 3: Resztak2022biorxiv_qtl rs1642796
#> 4: Resztak2022biorxiv_qtl rs1642797
#> 5: Resztak2022biorxiv_qtl rs12450254
#> ---
#> 260: Resztak2022biorxiv_qtl rs1393370347
#> 261: Resztak2022biorxiv_qtl rs373872446
#> 262: Resztak2022biorxiv_qtl rs1052202011
#> 263: Resztak2022biorxiv_qtl rs8070743
#> 264: Resztak2022biorxiv_qtl rs370880934
geneInfo <- xQTLquery_gene("TP53")
geneInfo <- xQTLquery_gene(c("tp53","naDK","SDF4") )
geneInfo <- xQTLquery_gene(c("ENSG00000210195.2","ENSG00000078808"))
geneInfo#> genes genesUpper geneSymbol gencodeId
#> 1: ENSG00000210195.2 ENSG00000210195.2 MT-TT ENSG00000210195.2
#> 2: ENSG00000078808 ENSG00000078808 SDF4 ENSG00000078808.16
#> entrezGeneId geneType chromosome start end strand tss
#> 1: NA Mt tRNA chrM 15888 15953 + 15888
#> 2: 51150 protein coding chr1 1216908 1232031 - 1232031
#> gencodeVersion genomeBuild
#> 1: v26 GRCh38/hg38
#> 2: v26 GRCh38/hg38
#> description
#> 1: mitochondrially encoded tRNA threonine [Source:HGNC Symbol;Acc:HGNC:7499]
#> 2: stromal cell derived factor 4 [Source:HGNC Symbol;Acc:HGNC:24188]
varInfo <- xQTLquery_varId("rs12596338")
varInfo <- xQTLquery_varId("chr11_66561248_T_C_b38")
varInfo <- xQTLquery_varPos(chrom="chr1", pos=c(1102708,1105739))
varInfo#> variantId snpId b37VariantId chromosome pos ref alt
#> 1: chr1_1102708_G_C_b38 rs66622470 1_1038088_G_C_b37 chr1 1102708 G C
#> datasetId maf01 shorthand
#> 1: gtex_v8 TRUE NA
tissueAll <- xQTLquery_tissue() # fetch all tissues in GTEx
Brain <- xQTLquery_tissue("Brain")
Brain#> colorHex colorRgb datasetId eGeneCount eqtlAgeMaxFemale eqtlAgeMaxMale
#> 1: EEEE00 238,238,0 gtex_v8 3726 70 70
#> 2: EEEE00 238,238,0 gtex_v8 5640 70 70
#> 3: EEEE00 238,238,0 gtex_v8 8362 70 70
#> 4: EEEE00 238,238,0 gtex_v8 10027 70 70
#> 5: EEEE00 238,238,0 gtex_v8 11240 70 70
#> 6: EEEE00 238,238,0 gtex_v8 9082 70 70
#> 7: EEEE00 238,238,0 gtex_v8 7335 70 70
#> 8: EEEE00 238,238,0 gtex_v8 5517 70 70
#> 9: EEEE00 238,238,0 gtex_v8 5499 70 70
#> 10: EEEE00 238,238,0 gtex_v8 8198 70 70
#> 11: EEEE00 238,238,0 gtex_v8 6902 70 70
#> 12: EEEE00 238,238,0 gtex_v8 4483 70 70
#> 13: EEEE00 238,238,0 gtex_v8 3301 70 70
#> eqtlAgeMeanFemale eqtlAgeMeanMale eqtlAgeMinFemale eqtlAgeMinMale
#> 1: 57.6 58.2 28 20
#> 2: 57.2 58.2 24 20
#> 3: 56.8 58.5 24 22
#> 4: 57.5 57.5 24 20
#> 5: 58.7 56.7 24 20
#> 6: 58.2 57.3 24 20
#> 7: 59.1 58.6 28 20
#> 8: 58.9 58.2 28 20
#> 9: 59.6 58.7 28 20
#> 10: 57.7 58.2 24 20
#> 11: 58.4 58.1 28 20
#> 12: 58.2 58.4 28 22
#> 13: 56.2 58.6 24 20
#> eqtlSampleCountFemale eqtlSampleCountMale expressedGeneCount hasEGenes
#> 1: 37 92 28196 TRUE
#> 2: 42 105 28921 TRUE
#> 3: 52 142 29230 TRUE
#> 4: 51 124 29538 TRUE
#> 5: 58 151 30106 TRUE
#> 6: 64 141 29560 TRUE
#> 7: 48 127 29132 TRUE
#> 8: 49 116 28625 TRUE
#> 9: 47 123 29502 TRUE
#> 10: 55 147 29339 TRUE
#> 11: 42 128 28335 TRUE
#> 12: 48 78 28352 TRUE
#> 13: 33 81 28050 TRUE
#> hasSGenes mappedInHubmap rnaSeqAgeMaxFemale rnaSeqAgeMaxMale
#> 1: TRUE FALSE 70 70
#> 2: TRUE FALSE 70 70
#> 3: TRUE FALSE 70 70
#> 4: TRUE FALSE 70 70
#> 5: TRUE FALSE 70 70
#> 6: TRUE FALSE 70 70
#> 7: TRUE FALSE 70 70
#> 8: TRUE FALSE 70 70
#> 9: TRUE FALSE 70 70
#> 10: TRUE FALSE 70 70
#> 11: TRUE FALSE 70 70
#> 12: TRUE FALSE 70 70
#> 13: TRUE FALSE 70 70
#> rnaSeqAgeMeanFemale rnaSeqAgeMeanMale rnaSeqAgeMinFemale rnaSeqAgeMinMale
#> 1: 57.2 58.9 28 20
#> 2: 57.2 58.8 24 20
#> 3: 56.9 59.2 24 22
#> 4: 57.3 58.5 24 20
#> 5: 58.3 57.3 24 20
#> 6: 57.8 58.2 24 20
#> 7: 58.7 59.1 28 20
#> 8: 58.3 58.8 28 20
#> 9: 59.3 59.0 28 20
#> 10: 57.7 58.8 24 20
#> 11: 58.4 58.5 28 20
#> 12: 58.1 59.7 28 22
#> 13: 56.2 59.3 24 20
#> rnaSeqAndGenotypeSampleCount rnaSeqSampleCount rnaSeqSampleCountFemale
#> 1: 129 152 45
#> 2: 147 176 48
#> 3: 194 246 63
#> 4: 175 215 58
#> 5: 209 241 67
#> 6: 205 255 74
#> 7: 175 209 56
#> 8: 165 197 54
#> 9: 170 202 55
#> 10: 202 246 64
#> 11: 170 205 49
#> 12: 126 159 57
#> 13: 114 139 38
#> rnaSeqSampleCountMale sGeneCount
#> 1: 107 892
#> 2: 128 1238
#> 3: 183 1809
#> 4: 157 2397
#> 5: 174 2786
#> 6: 181 2048
#> 7: 153 1684
#> 8: 143 1185
#> 9: 147 1414
#> 10: 182 1881
#> 11: 156 1350
#> 12: 102 1144
#> 13: 101 814
#> samplingSite
#> 1: Amygdala (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> 2: Anterior cingulate cortex (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> 3: Caudate (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> 4: Cerebellar hemisphere (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> 5: Right cerebellum (sampled at donor collection site and preserved in PAXgene fixative).
#> 6: Right cerebral frontal pole cortex (sampled at donor collection site and preserved in PAXgene fixative).
#> 7: Right cerebral frontal pole cortex (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> 8: Hippocampus (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> 9: Hypothalamus (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> 10: Nucleus accumbens basal ganglia (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> 11: Putamen basal ganglia (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> 12: Spinal cord (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> 13: Substantia nigra (sampled at Miami Brain Bank and preserved as fresh frozen tissue).
#> tissueSite tissueSiteDetail tissueSiteDetailAbbr
#> 1: Brain Brain - Amygdala BRNAMY
#> 2: Brain Brain - Anterior cingulate cortex (BA24) BRNACC
#> 3: Brain Brain - Caudate (basal ganglia) BRNCDT
#> 4: Brain Brain - Cerebellar Hemisphere BRNCHB
#> 5: Brain Brain - Cerebellum BRNCHA
#> 6: Brain Brain - Cortex BRNCTXA
#> 7: Brain Brain - Frontal Cortex (BA9) BRNCTXB
#> 8: Brain Brain - Hippocampus BRNHPP
#> 9: Brain Brain - Hypothalamus BRNHPT
#> 10: Brain Brain - Nucleus accumbens (basal ganglia) BRNNCC
#> 11: Brain Brain - Putamen (basal ganglia) BRNPTM
#> 12: Brain Brain - Spinal cord (cervical c-1) BRNSPC
#> 13: Brain Brain - Substantia nigra BRNSNG
#> tissueSiteDetailId uberonId
#> 1: Brain_Amygdala 0001876
#> 2: Brain_Anterior_cingulate_cortex_BA24 0009835
#> 3: Brain_Caudate_basal_ganglia 0001873
#> 4: Brain_Cerebellar_Hemisphere 0002037
#> 5: Brain_Cerebellum 0002037
#> 6: Brain_Cortex 0001870
#> 7: Brain_Frontal_Cortex_BA9 0009834
#> 8: Brain_Hippocampus 0001954
#> 9: Brain_Hypothalamus 0001898
#> 10: Brain_Nucleus_accumbens_basal_ganglia 0001882
#> 11: Brain_Putamen_basal_ganglia 0001874
#> 12: Brain_Spinal_cord_cervical_c-1 0006469
#> 13: Brain_Substantia_nigra 0002038
sampleInfo <- xQTLquery_sampleByTissue("Brain - Amygdala" )
sampleInfo <- xQTLquery_sampleByTissue(tissueSiteDetail="Liver", pathologyNotesCategories=TRUE)
sampleIds <- c("GTEX-11NUK-0011-R4a-SM-DO12B", "GTEX-11ONC-0011-R4b-SM-DO93H",
"GTEX-11DXY-0526-SM-5EGGQ", "GTEX-13OVJ-1026-SM-5IFGI")
sampleInfo <- xQTLquery_sampleBySampleId(sampleIds)
sampleInfo#> ageBracket aliquotId autolysisScore dataType datasetId
#> 1: 60-69 SM-5EGGQ Mild RNASEQ gtex_v8
#> 2: 50-59 SM-DO12B <NA> RNASEQ gtex_v8
#> 3: 60-69 SM-DO93H <NA> RNASEQ gtex_v8
#> 4: 50-59 SM-5IFGI Mild EXCLUDE gtex_v8
#> hardyScale ischemicTime ischemicTimeGroup
#> 1: Fast death - natural causes 891 601 - 900
#> 2: Fast death - natural causes 864 601 - 900
#> 3: Fast death - natural causes 587 301 - 600
#> 4: Fast death - natural causes 1129 901 - 1200
#> pathologyNotes rin
#> 1: 2 pieces, congestion 6.8
#> 2: <NA> 7.1
#> 3: <NA> 7.1
#> 4: 2 pieces; cirrhosis, steatosis, Mallory hyaline c/w alcoholic cirrhosis 6.2
#> sampleId sex subjectId tissueSampleId
#> 1: GTEX-11DXY-0526-SM-5EGGQ male GTEX-11DXY GTEX-11DXY-0526
#> 2: GTEX-11NUK-0011-R4a-SM-DO12B male GTEX-11NUK GTEX-11NUK-0011-R4a
#> 3: GTEX-11ONC-0011-R4b-SM-DO93H male GTEX-11ONC GTEX-11ONC-0011-R4b
#> 4: GTEX-13OVJ-1026-SM-5IFGI female GTEX-13OVJ GTEX-13OVJ-1026
#> tissueSiteDetail tissueSiteDetailId uberonId
#> 1: Liver Liver 0001114
#> 2: Brain - Amygdala Brain_Amygdala 0001876
#> 3: Brain - Amygdala Brain_Amygdala 0001876
#> 4: Liver Liver 0001114
eQTLexp <- xQTLdownload_eqtlExp(variantName="rs1641513",gene="TP53", tissueSiteDetail="Liver")
eQTLexp <- xQTLdownload_eqtlExp(variantName="chr1_14677_G_A_b38",gene="ENSG00000228463.9",
tissueSiteDetail="Stomach")
eQTLexp#> normExp genotypes
#> 1: -2.1600444 0
#> 2: 0.1509692 0
#> 3: 0.7464682 0
#> 4: -0.2613195 0
#> 5: 0.9212440 0
#> ---
#> 320: 0.9944579 0
#> 321: -0.9450852 0
#> 322: -0.7566981 0
#> 323: 1.3266775 0
#> 324: 0.8750651 0
sQTLratio <- xQTLdownload_sqtlExp(variantName="rs1450891501",
phenotypeId="chr1:497299:498399:clu_54863:ENSG00000239906.1",
tissueSiteDetail="Lung")
sQTLratio <- xQTLdownload_sqtlExp(variantName="chr1_1259424_T_C_b38",
phenotypeId=" chr1:1487914:1489204:clu_52051:ENSG00000160072.19",
tissueSiteDetail="Adipose - Subcutaneous")
sQTLratio#> normExp genotypes
#> 1: 1.39907974 0
#> 2: -0.02638638 0
#> 3: 1.43450451 1
#> 4: 0.25182051 0
#> 5: -1.94683842 2
#> ---
#> 577: 1.82050424 2
#> 578: 1.24869651 1
#> 579: 0.61319702 0
#> 580: -2.59815685 1
#> 581: -1.69950516 1
eGeneInfo <- xQTLdownload_egene(tissueSiteDetail="Prostate", recordPerChunk=2000)
eGeneInfo <- xQTLdownload_egene("TP53")
eGeneInfo#> gencodeId geneSymbol entrezGeneId geneType chromosome start
#> 1: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 2: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 3: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 4: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 5: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 6: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 7: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> end tss log2AllelicFoldChange empiricalPValue pValue
#> 1: 7687550 7687550 -0.680804 4.94757e-06 8.68606e-10
#> 2: 7687550 7687550 -0.500061 2.63392e-02 9.07463e-06
#> 3: 7687550 7687550 -0.501278 2.00743e-03 5.18785e-07
#> 4: 7687550 7687550 -0.359329 1.43349e-03 6.52895e-07
#> 5: 7687550 7687550 -1.243570 1.55063e-03 5.70716e-07
#> 6: 7687550 7687550 -0.541348 1.38551e-06 2.05198e-10
#> 7: 7687550 7687550 -0.550911 2.00129e-07 3.00426e-11
#> pValueThreshold qValue tissueSiteDetail datasetId
#> 1: 1.26507e-04 3.94849e-06 Adipose - Subcutaneous gtex_v8
#> 2: 1.52146e-04 1.03629e-02 Cells - Cultured fibroblasts gtex_v8
#> 3: 1.13047e-04 1.25547e-03 Esophagus - Mucosa gtex_v8
#> 4: 5.80918e-06 2.32936e-02 Kidney - Cortex gtex_v8
#> 5: 3.88929e-05 2.94618e-03 Pituitary gtex_v8
#> 6: 1.18255e-04 1.28231e-06 Skin - Not Sun Exposed (Suprapubic) gtex_v8
#> 7: 1.60112e-04 1.50952e-07 Skin - Sun Exposed (Lower leg) gtex_v8
sGeneInfo <- xQTLdownload_sgene(tissueSiteDetail="Liver")
sGeneInfo <- xQTLdownload_sgene(gene="DDX11", tissueSiteDetail="Liver" )
eGeneInfo#> gencodeId geneSymbol entrezGeneId geneType chromosome start
#> 1: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 2: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 3: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 4: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 5: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 6: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> 7: ENSG00000141510.16 TP53 7157 protein coding chr17 7661779
#> end tss log2AllelicFoldChange empiricalPValue pValue
#> 1: 7687550 7687550 -0.680804 4.94757e-06 8.68606e-10
#> 2: 7687550 7687550 -0.500061 2.63392e-02 9.07463e-06
#> 3: 7687550 7687550 -0.501278 2.00743e-03 5.18785e-07
#> 4: 7687550 7687550 -0.359329 1.43349e-03 6.52895e-07
#> 5: 7687550 7687550 -1.243570 1.55063e-03 5.70716e-07
#> 6: 7687550 7687550 -0.541348 1.38551e-06 2.05198e-10
#> 7: 7687550 7687550 -0.550911 2.00129e-07 3.00426e-11
#> pValueThreshold qValue tissueSiteDetail datasetId
#> 1: 1.26507e-04 3.94849e-06 Adipose - Subcutaneous gtex_v8
#> 2: 1.52146e-04 1.03629e-02 Cells - Cultured fibroblasts gtex_v8
#> 3: 1.13047e-04 1.25547e-03 Esophagus - Mucosa gtex_v8
#> 4: 5.80918e-06 2.32936e-02 Kidney - Cortex gtex_v8
#> 5: 3.88929e-05 2.94618e-03 Pituitary gtex_v8
#> 6: 1.18255e-04 1.28231e-06 Skin - Not Sun Exposed (Suprapubic) gtex_v8
#> 7: 1.60112e-04 1.50952e-07 Skin - Sun Exposed (Lower leg) gtex_v8
expProfiles <- xQTLdownload_exp("ENSG00000210195.2", tissueSiteDetail="Liver")
expProfiles <- xQTLdownload_exp("ENSG00000210195.2", tissueSiteDetail="Liver",
toSummarizedExperiment=TRUE)
# extract expression profile from SummarizedExperiment object:
expDT <- SummarizedExperiment::assay(expProfiles)
# extract samples' detail from SummarizedExperiment object:
sampleDT <- SummarizedExperiment::colData(expProfiles)
expProfiles <- xQTLdownload_exp(c("tp53","naDK","SDF4"),
tissueSiteDetail="Artery - Coronary",
pathologyNotesCategories=TRUE)
expProfiles <- xQTLdownload_exp(c("ENSG00000141510.16","ENSG00000008130.15","ENSG00000078808"),
tissueSiteDetail="Artery - Coronary")
expProfiles[,1:12]#> gencodeId genes geneSymbol datasetId tissueSiteDetailId
#> 1 ENSG00000141510.16 ENSG00000141510.16 TP53 gtex_v8 Artery_Coronary
#> 2 ENSG00000008130.15 ENSG00000008130.15 NADK gtex_v8 Artery_Coronary
#> 3 ENSG00000078808.16 ENSG00000078808 SDF4 gtex_v8 Artery_Coronary
#> unit genesUpper GTEX-1117F-0626-SM-5N9CS GTEX-1122O-0426-SM-5H12G
#> 1 TPM ENSG00000141510.16 27.83 16.88
#> 2 TPM ENSG00000008130.15 77.78 60.54
#> 3 TPM ENSG00000078808.16 210.60 205.60
#> GTEX-117YX-1726-SM-5GZZS GTEX-11DXX-0826-SM-5GZZP GTEX-11DXY-1126-SM-5987W
#> 1 20.25 24.36 20.53
#> 2 69.14 62.15 31.90
#> 3 203.60 184.10 188.60
geneMedExp <- xQTLdownload_geneMedExp(genes=c("TP53", "IRF5"))
geneMedExp#> gencodeId geneSymbol median tissueSiteDetail
#> 1: ENSG00000128604.19 IRF5 8.53482 Adipose - Subcutaneous
#> 2: ENSG00000128604.19 IRF5 6.12789 Adipose - Visceral (Omentum)
#> 3: ENSG00000128604.19 IRF5 4.67700 Adrenal Gland
#> 4: ENSG00000128604.19 IRF5 5.29194 Artery - Aorta
#> 5: ENSG00000128604.19 IRF5 6.60034 Artery - Coronary
#> ---
#> 104: ENSG00000141510.16 TP53 14.82610 Testis
#> 105: ENSG00000141510.16 TP53 19.66310 Thyroid
#> 106: ENSG00000141510.16 TP53 29.49970 Uterus
#> 107: ENSG00000141510.16 TP53 25.29200 Vagina
#> 108: ENSG00000141510.16 TP53 7.69810 Whole Blood
#> entrezGeneId geneType chromosome start end strand
#> 1: 3663 protein coding chr7 128937612 128950035 +
#> 2: 3663 protein coding chr7 128937612 128950035 +
#> 3: 3663 protein coding chr7 128937612 128950035 +
#> 4: 3663 protein coding chr7 128937612 128950035 +
#> 5: 3663 protein coding chr7 128937612 128950035 +
#> ---
#> 104: 7157 protein coding chr17 7661779 7687550 -
#> 105: 7157 protein coding chr17 7661779 7687550 -
#> 106: 7157 protein coding chr17 7661779 7687550 -
#> 107: 7157 protein coding chr17 7661779 7687550 -
#> 108: 7157 protein coding chr17 7661779 7687550 -
#> tss
#> 1: 128937612
#> 2: 128937612
#> 3: 128937612
#> 4: 128937612
#> 5: 128937612
#> ---
#> 104: 7687550
#> 105: 7687550
#> 106: 7687550
#> 107: 7687550
#> 108: 7687550