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Vdsukhov read gct #7

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merged 5 commits into from
Mar 27, 2024
Merged

Vdsukhov read gct #7

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e33f88a
Adjusted indexing in the data.table object
vdsukhov Mar 24, 2024
8eaa138
Merge branch 'main' into readGct
vdsukhov Mar 27, 2024
f2263bb
Merge branch 'main' into readGct
vdsukhov Mar 27, 2024
9db3f43
Added test for readGct with GSE141540
vdsukhov Mar 27, 2024
5ed6e2d
smaller test file
assaron Mar 27, 2024
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3 changes: 2 additions & 1 deletion R/gct.R
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Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,8 @@ readGct <- function(gct) {
rn <- make.unique(rn)
}

exp <- as.matrix(t[, (ann.row + 2):ncol(t)])
exp.cols <- (ann.row + 2):ncol(t)
exp <- as.matrix(t[, exp.cols, with=FALSE])
rownames(exp) <- rn


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20 changes: 20 additions & 0 deletions inst/extdata/testdata/gct/GSE141540.gct
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Original file line number Diff line number Diff line change
@@ -0,0 +1,20 @@
#1.3
10 6 9 7
id/title Gene ID Gene symbol Mean logFC AveExpr t P.Value adj.P.Val B Trp1 CD4+ TILs, Th condition sample 1 Trp1 CD4+ TILs, Th condition sample 2 Trp1 CD4+ TILs, Th condition sample 3 Trp1 CD4+ TILs, Th-ctx condition sample 1 Trp1 CD4+ TILs, Th-ctx condition sample 2 Trp1 CD4+ TILs, Th-ctx condition sample 3
geo_accession na na na na na na na na na GSM4205863 GSM4205864 GSM4205865 GSM4205866 GSM4205867 GSM4205868
tumour type na na na na na na na na na B16 melanoma B16 melanoma B16 melanoma B16 melanoma B16 melanoma B16 melanoma
tissue na na na na na na na na na tumour tumour tumour tumour tumour tumour
cell type na na na na na na na na na Foxp3GFP- CD4+ Trp-1 cells Foxp3GFP- CD4+ Trp-1 cells Foxp3GFP- CD4+ Trp-1 cells Foxp3GFP- CD4+ Trp-1 cells Foxp3GFP- CD4+ Trp-1 cells Foxp3GFP- CD4+ Trp-1 cells
condition na na na na na na na na na Trp1 CD4+ TILs, Th condition Trp1 CD4+ TILs, Th condition Trp1 CD4+ TILs, Th condition Trp1 CD4+ TILs, Th-ctx condition Trp1 CD4+ TILs, Th-ctx condition Trp1 CD4+ TILs, Th-ctx condition
replicate na na na na na na na na na 1 2 3 1 2 3
Comparison na na na na na na na na na Reference Reference Reference Target Target Target
1424733_at 140795 P2ry14 6.5372 2.5902 6.5372 22.565 5.6834e-8 0.00056834 8.5214 5.1463 5.1581 5.4219 7.7382 7.9779 7.7807
1454617_at 105171 Arrdc3 7.2280 1.6425 7.2280 16.489 5.2864e-7 0.0011748 6.8493 6.3730 6.5109 6.3363 7.9909 8.1878 7.9691
1417398_at 66922 Rras2 7.8840 1.7922 7.8840 16.300 5.7363e-7 0.0011748 6.7817 7.0530 6.8373 7.0735 8.7226 8.9318 8.6858
1453851_a_at 23882 Gadd45g 8.3413 1.7310 8.3413 15.727 7.3830e-7 0.0011748 6.5705 7.4854 7.4522 7.4898 9.3597 9.0003 9.2604
1425570_at 27218 Slamf1 10.426 1.6919 10.426 15.548 8.0041e-7 0.0011748 6.5021 9.4423 9.5518 9.7448 11.209 11.387 11.219
1444426_at 320664 Cass4 8.0858 2.7655 8.0858 15.402 8.5528e-7 0.0011748 6.4456 6.4620 6.9625 6.6846 9.6524 9.6129 9.1403
1421186_at 12772 Ccr2 10.542 2.8435 10.542 14.877 0.0000010916 0.0011748 6.2358 8.6917 9.4154 9.2545 11.902 12.137 11.853
1424638_at 12575 Cdkn1a 11.190 2.0431 11.190 14.841 0.0000011104 0.0011748 6.2210 9.8865 10.332 10.286 12.115 12.189 12.330
1424727_at 12774 Ccr5 10.375 2.7007 10.375 14.636 0.0000012246 0.0011748 6.1358 8.6012 9.3384 9.1356 11.742 11.811 11.624
1435436_at 13819 Epas1 9.1513 1.8468 9.1513 14.454 0.0000013374 0.0011748 6.0587 8.1762 8.2527 8.2547 9.8769 10.336 10.011
7 changes: 7 additions & 0 deletions tests/testthat/test-gct.R
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Expand Up @@ -51,3 +51,10 @@ test_that("writeGct and readGct support id column names", {
expect_identical(fData(es), fData(es2))
expect_identical(pData(es), pData(es2))
})


test_that("readGct column indexing works with GSE141540.gct file", {
gctFile <- system.file("extdata/testdata/gct/GSE141540.gct", package="phantasusLite")
expect_silent(es <- readGct(gctFile))
})

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