Hi
see in line
> -----Original Message-----
> From: R-help <r-help-boun...@r-project.org> On Behalf Of N Meriam
> Sent: Tuesday, January 8, 2019 3:08 PM
> To: r-help@r-project.org
> Subject: [R] Warning message: NAs introduced by coercion
>
> Dear all,
>
> I have a .csv file called df4. (15752 obs. of 264 variables).
> I apply this code but couldn't continue further other analyses, a warning
> message keeps coming up. Then, I want to determine max and min
> similarity values,
> heat map plot, cluster...etc
>
> > require(SNPRelate)
> > library(gdsfmt)
> > myd <- read.csv(file = "df4.csv", header = TRUE)
> > names(myd)[-1]
> myd[,1]
> > myd[1:10, 1:10]
> # the data must be 0,1,2 with 3 as missing so you have r
> > sample.id <- names(myd)[-1]
> > snp.id <- myd[,1]
> > snp.position <- 1:length(snp.id) # not needed for ibs
> > snp.chromosome <- rep(1, each=length(snp.id)) # not needed for ibs
> > snp.allele <- rep("A/G", length(snp.id)) # not needed for ibs
> # genotype data must have - in 3
> > genod <- myd[,-1]
> > genod[is.na(genod)] <- 3
> > genod[genod=="0"] <- 0
> > genod[genod=="1"] <- 2
> > genod[1:10,1:10]
> > genod <- as.matrix(genod)
matrix can have only one type of data so you probaly changed it to character by
such construction.
> > class(genod) <- "numeric"
This tries to change all "numeric" values to numbers but if it cannot it sets
it to NA.
something like
> head(iris)
Sepal.Length Sepal.Width Petal.Length Petal.Width Species
1 5.1 3.5 1.4 0.2 setosa
2 4.9 3.0 1.4 0.2 setosa
3 4.7 3.2 1.3 0.2 setosa
4 4.6 3.1 1.5 0.2 setosa
5 5.0 3.6 1.4 0.2 setosa
6 5.4 3.9 1.7 0.4 setosa
> ir <-head(iris)
> irm <- as.matrix(ir)
> head(irm)
Sepal.Length Sepal.Width Petal.Length Petal.Width Species
1 "5.1" "3.5" "1.4" "0.2" "setosa"
2 "4.9" "3.0" "1.4" "0.2" "setosa"
3 "4.7" "3.2" "1.3" "0.2" "setosa"
4 "4.6" "3.1" "1.5" "0.2" "setosa"
5 "5.0" "3.6" "1.4" "0.2" "setosa"
6 "5.4" "3.9" "1.7" "0.4" "setosa"
> class(irm) <- "numeric"
Warning message:
In class(irm) <- "numeric" : NAs introduced by coercion
> head(irm)
Sepal.Length Sepal.Width Petal.Length Petal.Width Species
1 5.1 3.5 1.4 0.2 NA
2 4.9 3.0 1.4 0.2 NA
3 4.7 3.2 1.3 0.2 NA
4 4.6 3.1 1.5 0.2 NA
5 5.0 3.6 1.4 0.2 NA
6 5.4 3.9 1.7 0.4 NA
>
Cheers
Petr
>
>
> *Warning message:In class(genod) <- "numeric" : NAs introduced by coercion*
>
> Maybe I could illustrate more with details so I can be more specific?
> Please, let me know.
>
> I would appreciate your help.
> Thanks,
> Meriam
>
> [[alternative HTML version deleted]]
>
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