Did you work the examples in help("merge")? Also, have you looked at
the "dplyr" package? It has 9 different vignettes. The lead author is
Hadley Wickham, who won the 2019 COPSS Presidents' Award for work like
this.
Alternatively, you could manually read all 10 files, then figure out
from that what the merged object should look like with what rows and
what columns.
I might start with something like:
PosAll <- unique(c(table1$Pos, table2$Pos, ... ))
Combined <- data.frame(Pos=PosAll, col1=NA, col2=NA, ...)
Then create the object you want that contains a column "Pos" =
PosAll. Then:
rownames(table1) <- table1$Pos
rownames(table2) <- table2$Pos
...
sel1 <- PosAll %in% table1$Pos
...
Combined[sel1, names(table1)] <- table1[PosAll[sel1], ]
CAVEAT: I haven't tried this exact code. It may not work as
written. However, I've done things like this in the past. "merge" and
"dplyr" have seemed too much like black magic for me.
Spencer
On 2020-12-15 16:13, pooja sinha wrote:
I know that but I do not want to merge them sequentially because I may lose
some rows which are present in one file while the other doesn't have. I
googled and found something called multmerge but the code is not working
for me. I used the following:
path <-"P:/Documents/Puja Desktop items/Documents/RESULTS/est meth
results/Final_est_meth_data_rn6/WGBS_exon_sort_CHG/merge_csv"
filenames <- list.files(path = path)
View(filenames)
multmerge = function(path){
filenames=list.files(path=path, full.names=TRUE)
datalist = lapply(filenames, function(x){read.csv(file=x,header=T)})
Reduce(function(x,y) {merge(x,y)}, datalist)
}
full_data = multmerge("~/P:/Documents/Puja Desktop
items/Documents/RESULTS/est meth
results/Final_est_meth_data_rn6/WGBS_exon_sort_CHG/merge_csv")
But after running the full_data, the folder is empty.
Thanks,
Puja
On Tue, Dec 15, 2020 at 4:51 PM Bert Gunter <bgunter.4...@gmail.com> wrote:
?read.csv to read your csv files in data frames
?merge to merge them (sequentially).
Bert Gunter
"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
On Tue, Dec 15, 2020 at 1:36 PM pooja sinha <pjsinh...@gmail.com> wrote:
Hi All,
I have 10 .csv files containing 12 to 15 columns but have some columns in
common. I need to join all of my .csv files into one using one common
column ‘Pos’. The header portion of my .csv files looks as shown below:
Chrom Pos Avg Stdev A15_3509.C A31_3799.C A32_3800.C A35_3804.C Gene ID
Class ExNum
Can anyone help me in getting the code for the above problem. Any help
will be highly appreciated.
Thanks,
Puja
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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