Description Usage Arguments Details Value Author(s) See Also Examples
For some analyses you might be interested in transforming the counts into RPKMs which you can do with this function.
1 |
rse |
A RangedSummarizedExperiment-class object as downloaded with download_study. |
length_var |
A length 1 character vector with the column name from
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mapped_var |
A length 1 character vector with the column name from
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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
scale_counts
1 2 3 4 5 6 7 8 9 10 11 | ## 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)
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