I am attempting to created colClasses for several tables, then read only
specific columns. There are two different table layouts that I am working with.
If I use exclusively one layout, the script works perfectly, but if I mix the
layouts, it fails to grab the correct columns form layout that is read in
second. It appears that colClasses fails to adopt the new structure after the
first iteration. Is there some way to clear colClasses of flush the write
buffer between iterations?
Thanks,
Aaron
for(i in 1:length(fullnames.in))
{
cnames<- read.table(fullnames.in[i], header=FALSE, sep="\t",
na.strings="", nrows=1, row.names = NULL
, skip=9, fill=TRUE, quote="")
#initialize col.classes to NULL vector
seq(1,length(cnames))->column.classes
column.classes[1:length(cnames)]="NULL"
#find where the desired columns are
idx<-which(cnames=="Row")
column.classes[idx]="integer"
idx<-which(cnames=="Col")
column.classes[idx]="integer"
idx<-which(cnames=="ControlType")
column.classes[idx]="integer"
idx<-which(cnames=="ProbeName")
column.classes[idx]="character"
idx<-which(cnames=="GeneName")
column.classes[idx]="character"
idx<-which(cnames=="SystematicName")
column.classes[idx]="character"
idx<-which(cnames=="LogRatio")
column.classes[idx]="numeric"
idx<-which(cnames=="gMeanSignal")
column.classes[idx]="numeric"
idx<-which(cnames=="rMeanSignal")
column.classes[idx]="numeric"
idx<-which(cnames=="gBGMeanSignal")
column.classes[idx]="numeric"
idx<-which(cnames=="rBGMeanSignal")
column.classes[idx]="numeric"
print(fullnames.in[i])
print("Reading file, this could take a few minutes")
#read all rows of selected columns into data.frame
d <- read.table(fullnames.in[1], header=TRUE, sep="\t",
na.strings="", nrows=number.rows, colClasses=column.classes, row.names = NULL
, skip=9, fill=TRUE, quote="")
print("Writing file, this could take a few minutes")
#write all rows of selected columns into file
write.table(d, fullnames.out[i], sep="\t", quote=FALSE,
row.names=FALSE)
rm(cnames, column.classes, d, idx)
}
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