Question: rowVars function, used in ballgown analysis not available for R 3.5.2, alternatives?
1
gravatar for RNAseqer
7 months ago by
RNAseqer 110
RNAseqer 110 wrote:

Hello,

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: https://rpubs.com/kapeelc12/Ballgown

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
5
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 ?

install.packages('metaMA')
library(metaMA)
?rowVars
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

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ADD REPLYlink written 7 months ago by WouterDeCoster41k
4
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
1

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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