Question: rowVars function, used in ballgown analysis not available for R 3.5.2, alternatives?
gravatar for RNAseqer
7 months ago by
RNAseqer 110
RNAseqer 110 wrote:


I've hit a bit of a snag here: I had to update to the latest version of R to get ballgown working, but one of the functions I see included in filtering out low expression genes, rowVars, is not available for this version of R.

Using this tutorial:

The rowVars function is employed in filtering:

bg_filt = subset(bg,"rowVars(texpr(bg)) >1",genomesubset=TRUE)

I have R studio, would it be possible to download an older version of R and switch to it temporarily to use rowVars, then switch back to continue the ballgown output analysis?

If so does anyone know what the last version of R rowVars worked on?

Or should I try to find an older version of ballgown, and downgrade my R version? I know there are many functions on bioconductor that do not necessarily work on the latest version of R, so is there a benifit to running older versions of R generally when working with these packages?

rowvars rna-seq ballgown R • 579 views
ADD COMMENTlink modified 7 months ago by kristoffer.vittingseerup2.4k • written 7 months ago by RNAseqer 110
gravatar for Bastien Hervé
7 months ago by
Bastien Hervé4.4k
Limoges, CBRS, France
Bastien Hervé4.4k wrote:

Is it the rowVars function from metaMA ?

ADD COMMENTlink written 7 months ago by Bastien Hervé4.4k

Huh, must be! I tried to get it as part of matrixstats but that didnt work, this download did. Thanks a bunch! This was a real help.

ADD REPLYlink written 7 months ago by RNAseqer 110

This comment has been moved to an answer so it can get accepted and mark this question as solved.

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

ADD REPLYlink written 7 months ago by WouterDeCoster41k
gravatar for kristoffer.vittingseerup
7 months ago by
European Union
kristoffer.vittingseerup2.4k wrote:

I would not recommend using ballgown in the first place - it performs VERY poorly compared to all the other DE tools out there (and have not been updated in years). Take a look at this recent benchmark (which agrees with most other benchmarks but is one of the few that actually test ballgown). Instead go for DESeq2 or edgeR - if you have StringTie data you can directly get them into R via tximport and use use DESeq2 as described here.

ADD COMMENTlink modified 6 months ago • written 7 months ago by kristoffer.vittingseerup2.4k

This is going to save me some time and heartache. Thanks for the heads-up!

ADD REPLYlink written 7 months ago by RNAseqer 110
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