[R] Recoding variables based on reference values in data frame

[Rui Barradas]

Hello,

I'm not sure I understood, but try the following.


Kgeno <- read.table(text = "
SNP_ID SNP1 SNP2 SNP3 SNP4
Maj_Allele C G  C  A
Min_Allele T A T G
ID1 CC     GG     CT     AA
ID2 CC     GG     CC AA
ID3 CC     GG    nc    AA
ID4 _ _ _ _
ID5 CC     GG     CC     AA
ID6 CC     GG     CC     AA
ID7 CC     GG     CT     AA
ID8 _ _ _ _
ID9 CT     GG     CC AG
ID10 CC     GG     CC     AA
ID11 CC     GG     CT     AA
ID12 _ _ _ _
ID13 CC     GG     CC     AA
", header = TRUE, stringsAsFactors = FALSE)

dat

fun <- function(x){
	x[x %in% c("nc", "_")] <- NA
	MM <- paste0(x[1], x[1])  # Major Major
	Mm <- paste0(x[1], x[2])  # Major minor
	mm <- paste0(x[2], x[2])  # minor minor
	x[x == MM] <- 0
	x[x == Mm] <- 1
	x[x == mm] <- 2
	x
}

Kgeno[, -1] <- sapply(Kgeno[, -1], fun)
Kgeno


Also, the best way to post data is by using ?dput.

dput(head(Kgeno[, 1:5], 30))  # post the output of this


Hope this helps,

Rui Barradas

Em 02-07-2013 21:46, kathleen askland escreveu:
> I'm new to R (previously used SAS primarily) and I have a genetics data
> frame consisting of genotypes for each of 300+ subjects (ID1, ID2, ID3,
> ...) at 3000+ genetic locations (SNP1, SNP2, SNP3...). A small subset of
> the data is shown below:
>    SNP_ID SNP1 SNP2 SNP3 SNP4  Maj_Allele C G  C  A  Min_Allele T A T G  ID1
> CC     GG     CT     AA      ID2 CC     GG     CC AA      ID3 CC     GG
> nc
> AA      ID4 _ _ _ _  ID5 CC     GG     CC     AA      ID6 CC     GG     CC
>       AA      ID7 CC     GG     CT     AA      ID8 _ _ _ _  ID9 CT     GG
> CC AG      ID10 CC     GG     CC     AA      ID11 CC     GG     CT     AA
>        ID12 _ _ _ _  ID13 CC     GG     CC     AA
> The name of the data file is Kgeno.
> What I would like to do is recode all of the genotype values to standard
> integer notation, based on their values relative to the reference rows
> (Maj_Allele and Min_Allele). Standard notation sums the total of minor
> alleles in the genotype, so values can be 0, 1 or 2.
>
> Here are the changes I want to make:
> 1. If the genotype= "nc" or '_" then set equal to NA.
> 2. If genotype value = a character string comprised of two consecutive
> major allele values -- c(Maj_Allele, Maj_Allele) -- then set equal to 0.
> 3. If genotype  value= c(Maj_Allele, Min_Allele) then set equal to 1.
> 4. If genotype  value = c(Min_Allele, Min_Allele) then set equal to 2.
>
> I've tried the following ifelse processing but get error (Warning: Executed
> script did not end with R session at the top-level prompt.  Top-level state
> will be restored) and can't seem to fix the code properly. I've counted the
> parentheses. Also, not sure if it would execute properly if I could fix it.
>
> # change 'nc' and '_' to NA, else leave as is:
> Kgeno[,2] <- ifelse(Kgeno[,2] == "nc", "NA", Kgeno[,2])
> Kgeno[,2] <- ifelse(Kgeno[,2] == "_", "NA", Kgeno[,2])
>
> #convert genotype strings in the first data column to numeric values #(two
> major alleles=0, 1 minor and 1 major=1, 2 minor alleles=2), else #leave as
> is (to preserve NA values).
>
> Kgeno[,2] <-
>
> ifelse(Kgeno[,2] == noquote(paste(as.character(Kgeno[1,2]), as.character(
> Kgeno[1,2]), sep=""), 0,
>
> ifelse(Kgeno[,2] == noquote(paste(as.character(Kgeno[1,2]), as.character(
> Kgeno[2,2]), sep=""), 1,
>
> ifelse(Kgeno[,2] == noquote(paste(as.character(Kgeno[2,2]), as.character(
> Kgeno[2,2]), sep=""), 2,
>              Kgeno[,2])))
>
>
> Finally, if above code were corrected, this would only change the first
> column of data, but I would like to change all 3000+ columns in the same
> way.
>
> I would greatly appreciate some suggestions on how to proceed.
>
> Thank you,
>
> Kathleen
>
> ---
> Kathleen Askland, MD
> Assistant Professor
> Department of Psychiatry & Human Behavior
> The Warren Alpert School of Medicine
> Brown University/Butler Hospital
>
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>
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