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blahah/gene_counts.R

Created April 7, 2014 13:21
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extract gene counts from transcript ID/count
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gene_counts.R
# convert transcript ID to gene ID
df <- data.frame(a = c("AT1G2.1", "AT1G2.3", "AT1G2.3", "AT1G3.1", "AT1G3.3", "AT1G3.3"), b=1:6)
df$t <- gsub(df$a, pattern="\\.[0-9]+", replacement="")
# sum by gene ID
aggregate(df[,2], by=list(as.factor(df$t)), sum)
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blahah commented Apr 7, 2014

NOTE: Please don't ever just sum transcript counts to get gene counts in a real analysis. This code is just to demonstrate gsub and aggregate to a colleague.

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