Comments interspersed, and some code at the end.
On Mon, 5 Mar 2018, Sariya, Sanjeev wrote:
Thanks. I think nabble is good for programming questions. Bear with me
if I'm incorrect.
You may have found R-help archives at Nabble, but R-help has nothing to do
with Nabble.
Data: Genomics SNP information
I know almost nothing about using R for genomics.
Goal: I need to add Chromosome and SNP position to the data frame I'm using
through apply.
I'd like to add new column from text processed through apply function.
For example: 10:60523:T:G (Column 2)
CHR: 10
Position: 60523
Assuming Position is "P", what are your "SNP" and "BP" in the names you
assigned below as c("SNP","P","CHR","BP")?
Dataset:
chr rs ps n_miss allele1 allele0 af beta se l_remle
p_wald
-9 10:60523:T:G -9 0 T G 0.977 -1.769354e-02
3.597196e-02 1.566731e-01 6.228309e-01
-9 10:60684:A:C -9 0 A C 0.973 1.698925e-02
2.942366e-02 1.561001e-01 5.636926e-01
-9 10:61331:A:G -9 0 A G 0.973 1.708586e-02
2.942424e-02 1.560944e-01 5.614851e-01
-9 10:62010:C:T -9 0 C T 0.980 -8.513143e-03
3.837054e-02 1.566875e-01 8.244260e-01
Code:
--------------------------------------------------------
data<-read.table("small.txt",header = T) # read data
data<-data[,c(2,11)] #delete other columns not needed
#--split data on : and get chromosome and position
split_rs<-function(rs){
chr<-vector(,length(rs)) # create new vector to store chr
pos<-vector(,length(rs)) #create new vector to store position
for(i in 1:length(rs)){ #iterate over RS column
if(grepl(":",rs[i])){ #if : in column string
temp <- strsplit(rs[i],":",fixed=T) #split
chr[i] <-temp[[1]][1] #store CHR
pos[i] <- temp[[1]][2] #store position
}
}
return(list(chr=chr,pos=pos)) #return making a list
}
data$POS<-"NA" #add new column CHR and make NA
data$CHR <- "NA" #add new column POS and make NA
temp<-apply(data,2,split_rs) #send data frame to function
#--I assign value from list sent -- I would like to improve this part
data$CHR<-temp$rs$chr
data$POS<-temp$rs$pos
rm(temp)
colnames(data)<-c("SNP","P","CHR","BP")
--------------------------------------------------------
######################################################
# Your code was pretty severely broken... it would not run,
# and I don't know what you expected to see as output.
# 1) data is the name of a function in base R... re-using
# it can lead to puzzling errors
# 2) With all this character manipulation, you need to read
# your character data in as character, not as factors
# 3) Don't use the T variable... use the constant TRUE,
# since T can easily be overwritten to some non-TRUE value.
dta <- read.table( "small.txt", header = TRUE, as.is = TRUE ) # read data
dta <- dta[ , c( 2, 11 ) ] #delete other columns not needed
# 4) Not at all clear why you want to split all of the columns
# using apply( ..., 2, ... ) when only one column has ":" characters
#temp <- apply( dta, 2, split_rs ) #send data frame to function
temp <- strsplit( dta$rs, ":" ) # gets the whole column splits at once
# wildly guessing here
rs_chrmatrix <- do.call( rbind, temp )
rs_DF <- as.data.frame( rs_chrmatrix, stringsAsFactors = FALSE )
names( rs_DF ) <- c( "CHR", "P", "X1", "X2" )
rs_DF$P <- as.integer( rs_DF$P )
str( rs_DF )
##################################################
-----Original Message-----
From: Jeff Newmiller [mailto:jdnew...@dcn.davis.ca.us]
Sent: Monday, March 5, 2018 1:48 PM
To: r-help@r-project.org; Sariya, Sanjeev <ss5...@cumc.columbia.edu>; R Help
<r-help@r-project.org>
Subject: Re: [R] Help with apply and new column?
Read the Posting Guide... (see message footer) ... some relevant things you can
find there:
a) Yes, this appears to be about how to use an R base function so it is on topic
b) Post a reproducible example (include some sample data, preferably using the
dput function)
c) Post using plain text so the mailing list doesn't convert it for you and
mangle things in a way you did not intend.
--
Sent from my phone. Please excuse my brevity.
On March 5, 2018 10:07:24 AM PST, "Sariya, Sanjeev" <ss5...@cumc.columbia.edu>
wrote:
Hello members,
Can I ask question for apply, adding new column to data frame on this
e-mail list?
Thanks!
[[alternative HTML version deleted]]
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