Question: How to get missing columns in DEXSeq analysis (exon usage coefficients)
0
6 months ago by
mjrarcher0 wrote:

Dear all,

I have been running DEXSeqAlt to perform differential exon usage analysis of a large cohort. I have three conditions in my metadata table. After calling the function DEXSeqResults (dxd), the result I obtained had all columns as shown in the vignette, but my conditions and the foldchange values. Can anyone please explain why this might be?

dexseq dexseqalt • 192 views
written 6 months ago by mjrarcher0

Could you send me a small reproducible example code along with a small data example (It could be, for example, the first 100 exons of your object)?

Alejandro

Hi Alejandro, I'm not sure how to send a reproducible example. I'll look into how I can do that, but in the mean time here is the code I used and the result I got:

#library('DEXSeqAlt')
# reducedModel <- ~ sample + exon
# fullModel <- ~ sample + exon + condition:exon
# dxd <- DEXSeqDataSetFromHTSeq(countfiles, sampleData=sampleTable, design= ~ sample + exon + condition:exon, flattenedfile = gf$# dxd <- estimateSizeFactors(dxd) # dxd <- estimateDispersionsAlt( dxd, formula = fullModel ) # dxd <- testForDEUAlt(dxd, reducedModel=reducedModel, fullModel=fullModel, verbose=FALSE ) # dxd = estimateExonFoldChanges( dxd, fitExpToVar="condition") # dxr1 <- DEXSeqResultsAlt(dxd) mcols(dxr1)$description

[1] "mean of the counts across samples in each feature/exon"
[2] "feature/exon identifier"
[3] "group/gene identifier"
[4] "exon dispersion estimate"
[5] "P-value of likelihood ratio test"
[7] "GRanges object of the coordinates of the exon/feature"
[8] "matrix of integer counts, of each column containing a sample"
[9] "list of transcripts overlapping with the exon

ADD REPLYlink modified 5 months ago by Martin Morgan ♦♦ 23k • written 5 months ago by mjrarcher0

As you can see, this is different from the values in the vignette (i'm missing columns 8, 9, and 10 in the above result):

mcols(dxr1)\$description
## [1] "group/gene identifier"
## [2] "feature/exon identifier"
## [3] "mean of the counts across samples in each feature/exon"
## [4] "exon dispersion estimate"
## [5] "LRT statistic: full vs reduced"
## [6] "LRT p-value: full vs reduced"
## [8] "exon usage coefficient"
## [9] "exon usage coefficient"
## [10] "relative exon usage fold change"
## [11] "GRanges object of the coordinates of the exon/feature"
## [12] "matrix of integer counts, of each column containing a sample"
## [13] "list of transcripts overlapping with the exon"

ADD REPLYlink modified 5 months ago by Martin Morgan ♦♦ 23k • written 5 months ago by mjrarcher0