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rlogarithmffffbase

log2 transform ff objects

I would like to log2 transform all numeric values in a ff object from ffpackage.

Using my df:

library(ff)
    df <- 'probeset_id sample1 sample2 sample3
            probe_1 1834.2 1743.4 1384
            probe_2 4711 4922 4650
            probe_3 4555 1387 4650.8
            probe_4 2588 1325 3258'
    df <- read.table(text=df, header=T)
    write.table(df, "del.txt", col.names=T, row.names=F, quote=F, sep="\t")
    df <- read.table.ffdf(file="del.txt", header=T)

I tried the below code but I got an error:

df[, 2:length(df)] <- log(df[2:length(df)], 2)
Error in log(df[2:length(df)], 2) :
  non-numeric argument to mathematical function

There exist a way to apply this funtion to ff objects?

Solution

  • log(df[,2:length(df)],2) works but sapply(df[,2:length(df)],log2) might work better if you've a big dataframe.