[R] Warning message: NAs introduced by coercion

[PIKAL Petr]

Hi

see in line

> -----Original Message-----
> From: R-help <r-help-bounces using r-project.org> On Behalf Of N Meriam
> Sent: Tuesday, January 8, 2019 3:08 PM
> To: r-help using 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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