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Exploratory analysis with scVI
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slowkow
/ rpkm_versus_tpm.R
Created
December 8, 2015 16:14
Comparison of RPKM (reads per kilobase per million) and TPM (transcripts per million).
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| # RPKM versus TPM | |
| # | |
| # RPKM and TPM are both normalized for library size and gene length. | |
| # | |
| # RPKM is not comparable across different samples. | |
| # | |
| # For more details, see: http://blog.nextgenetics.net/?e=51 | |
| rpkm <- function(counts, lengths) { | |
| rate <- counts / lengths |
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| # Installation (only needs to be done once) | |
| source("http://bioconductor.org/biocLite.R") | |
| biocLite("rhdf5") | |
| install.packages("devtools") | |
| devtools::install_github("pachterlab/sleuth") | |
| # Now load the package | |
| library("sleuth") | |
| # A function (borrowed from the Sleuth documentation) for connecting Ensembl transcript names to common gene names |