Thank you for your kind reply, that is most helpful, thank you, Victoria
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v.johnson •
Quick code question in TPM conversion from raw counts RNAseq
I am using the below code to calculate TPM which I found on GitHub. Can anyone just confirm please what the '2' in the tpms code equates to please? I am new to RNAseq and normalisation analysis and what to understand the code fully.
Thank you kindly
`tpm <- function(counts, lengths) { rate <- counts / lengths rate / sum(rate) * 1e6 }
tpms <- apply(counts, 2, function(x) tpm(x, genes$Length))`
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v.johnson •
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It is the argument (MARGIN) of the apply function; i.e. apply the tpm function to each column (2) of a data frame or matrix
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andres.firrincieli
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