Add rowRanges to DESeqDataSet

[zauhar]

Hi All,

I have imported htseq-count data using the DESeqDataSetFromHTSeqCount function in DESeq2, and for a test I wanted to generate FPKMs from the count data.

However, that requires rowRanges, and that attribute is present but has no content. The htseq-count data just has gene names and counts, I clearly need to use the GTF to add the ranges.

I have looked literally half the day for some example of actually adding the rowRanges - the tutorial examples for DeSeq2 used canned examples with the ranges already there, I can't find any examples of how to do it from scratch.

I can figure out how to add it, but surely for something so basic there is a function already available somewhere.

Thanks!
Randy

[zahrahaider]

Same Issue

I have exactly the same issue as @zauhar.

I need to calculate fpkm values and have made dds from HTSeq count. The rowranges in the resulting dds is NULL since the dds lacks the gene lengths.

So anybody out there who can help us!