Thank you, that helps.
-----Original Message-----
From: Jeff Newmiller [mailto:jdnew...@dcn.davis.ca.us]
Sent: Monday, March 5, 2018 3:36 PM
To: Sariya, Sanjeev <ss5...@cumc.columbia.edu>
Cc: r-help@r-project.org; R Help <r-help@r-project.org>
Subject: RE: [R] Help with apply and new column?
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]]
>>
>> ______________________________________________
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
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