makeAbundanceExport.RdAssemble a data.frame containing raw abundances of features that
are significant in at least one comparison.
makeAbundanceExport(testresList, abundancePrefix)List of data.frames with test results, typically
generated by runTest().
Character vector giving the prefix(es) of the columns in the test result tables that contain abundance information.
A data.frame with abundances for significant features.
sce <- readRDS(system.file("extdata", "mq_example", "1356_sce.rds",
package = "einprot"))
names(S4Vectors::metadata(sce)$testres$tests)
#> [1] "Chd4BF_vs_Adnp" "Adnp_vs_RBC_ctrl" "Chd4BF_vs_RBC_ctrl"
abExp <- makeAbundanceExport(S4Vectors::metadata(sce)$testres$tests,
abundancePrefix = "iBAQ")
head(abExp)
#> pid showInVolcano_Chd4BF_vs_Adnp showInVolcano_Adnp_vs_RBC_ctrl
#> 1 Dhx9 FALSE TRUE
#> 2 Zmynd8 FALSE FALSE
#> 3 Zmym4 FALSE TRUE
#> 4 Rlf FALSE TRUE
#> 5 Atp5c1 TRUE NA
#> 6 Adnp FALSE TRUE
#> showInVolcano_Chd4BF_vs_RBC_ctrl iBAQ.Adnp.avg iBAQ.Chd4BF.avg
#> 1 TRUE 7.048067e+05 121103.0
#> 2 TRUE 4.112933e+03 159303.3
#> 3 TRUE 2.005813e+06 11268213.3
#> 4 FALSE 3.704467e+05 942932.0
#> 5 TRUE 0.000000e+00 1174223.3
#> 6 TRUE 2.954467e+08 189706666.7
#> iBAQ.RBC_ctrl.avg iBAQ.Adnp.sd iBAQ.Chd4BF.sd iBAQ.RBC_ctrl.sd iBAQ.Adnp_IP04
#> 1 0 4.332023e+05 79277.34 0.0 4.1330e+05
#> 2 0 3.805447e+03 53932.13 0.0 4.8299e+03
#> 3 0 2.066075e+06 19263730.12 0.0 8.7657e+05
#> 4 0 3.949380e+05 1617559.84 0.0 1.8078e+05
#> 5 0 0.000000e+00 1142004.04 0.0 0.0000e+00
#> 6 1222710 1.349137e+08 77346910.30 207015.6 2.0709e+08
#> iBAQ.Adnp_IP05 iBAQ.Adnp_IP06 iBAQ.Chd4BF_IP07 iBAQ.Chd4BF_IP08
#> 1 1202600 4.9852e+05 30009 174480
#> 2 0 7.5089e+03 215090 155380
#> 3 750470 4.3904e+06 188320 33512000
#> 4 106120 8.2444e+05 0 2810700
#> 5 0 0.0000e+00 624740 2487100
#> 6 228510000 4.5074e+08 154760000 278360000
#> iBAQ.Chd4BF_IP09 iBAQ.RBC_ctrl_IP01 iBAQ.RBC_ctrl_IP02 iBAQ.RBC_ctrl_IP03
#> 1 158820 0 0 0
#> 2 107440 0 0 0
#> 3 104320 0 0 0
#> 4 18096 0 0 0
#> 5 410830 0 0 0
#> 6 136000000 987130 1375600 1305400