Hello,
I have a list of four files. Each file is a list of gene models, and each
gene model has attributes in file columns. The sample_week-over-sample_week
fold change value foreach i in file is in column 5. The gene model ID is in
column 1. To make it more complicated, each gene i may not be found in all
four files. I've written R scripts to try to 1) write a function to iterate
over each file in the working directory, 2) if a gene model, i, is missing
in a file(x), paste an "NA" as the value for that key and 3) make one
master file from the four files with column names as indicated below in the
code.
function(g)(
for( i in x){
if( i == NULL)
print( text("NA"))
else( print(x[i,5])) #Fold-change value
))
files <- list.files( path=getwd(), pattern="*.txt", full.names=T,
recursive=FALSE)
lapply( files, function(x) {
x <- read.table( x, header=T) # load file
# apply function
out <- function(g)
# write to file
write.table( out, "myfile.txt", sep="\t", quote=F, row.names=F, col.names=T)
colnames(out)[1] = "ca02"
colnames(out)[2] = "ca24"
colnames(out)[3] = "ca48"
colnames(out)[4] = "ca812"
})
})
The code has no errors, but the file doesn't write to my working directory.
I don't think this path is the problem either.
I've seen the do.call function, thinking this may be the way to go.
Also, if I'd like to add a third column to the master file from the four
files, for example, the BLAST description for that gene model, i, in column
7, how to handle this command as well? I'm kinda new to R but hit a wall
when it comes to this level, as I have had no classroom training on writing
code. Hopefully, I can break on through with your assistance. Thanks much
and have a nice day.
--
Franklin
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