getRPKM {recount} | R Documentation |
For some analyses you might be interested in transforming the counts into RPKMs which you can do with this function.
getRPKM(rse, length_var = "bp_length", mapped_var = NULL)
rse |
A RangedSummarizedExperiment-class object as downloaded with download_study. |
length_var |
A length 1 character vector with the column name from
|
mapped_var |
A length 1 character vector with the column name from
|
For gene RSE objects, you will want to specify the length_var
because otherwise you will be adjusting for the total gene length instead
of the total exonic sequence length of the gene.
A matrix with the RPKM values.
Andrew Jaffe, Leonardo Collado-Torres
## get RPKM matrix rpkm <- getRPKM(rse_gene_SRP009615) ## You can also get an RPKM matrix after running scale_counts() ## with similar RPKM values rpkm2 <- getRPKM(scale_counts(rse_gene_SRP009615)) rpkm3 <- getRPKM(scale_counts(rse_gene_SRP009615, by = 'mapped_reads')) summary(rpkm - rpkm2) summary(rpkm - rpkm3) summary(rpkm2 - rpkm3)