I see...
Here's a portion of what my data looks like (csv file attached).
I run again and here are the results:
df4 <- read.csv(file = "mydata.csv", header = TRUE)
> require(SNPRelate)> library(gdsfmt)> myd <- df4> myd <- df4>
> names(myd)[-1][1] "marker" "X88" "X9" "X17" "X25"
> myd[,1][1] 3 4 5 6 8 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
> genod2 <- as.matrix(genod)> head(genod2) marker
> X88 X9 X17 X25
[1,] "100023173|F|0-47:G>A-47:G>A" "0" "3" "3" "3"
[2,] "1043336|F|0-7:A>G-7:A>G" "2" "0" "3" "0"
[3,] "1212218|F|0-49:A>G-49:A>G" "0" "0" "0" "0"
[4,] "1019554|F|0-14:T>C-14:T>C" "0" "0" "3" "0"
[5,] "100024550|F|0-16:G>A-16:G>A" "3" "3" "3" "3"
[6,] "1106702|F|0-8:C>A-8:C>A" "0" "0" "0" "0"
> class(genod2) <- "numeric"Warning message:In class(genod2) <- "numeric" : NAs
> introduced by coercion> head(genod2)
marker X88 X9 X17 X25
[1,] NA 0 3 3 3
[2,] NA 2 0 3 0
[3,] NA 0 0 0 0
[4,] NA 0 0 3 0
[5,] NA 3 3 3 3
[6,] NA 0 0 0 0
> class(genod2) <- "numeric"> class(genod2)[1] "matrix"
> # read data > filn <-"simTunesian.gds"> snpgdsCreateGeno(filn, genmat =
> genod,+ sample.id = sample.id, snp.id = snp.id,+
> snp.chromosome = snp.chromosome,+ snp.position =
> snp.position,+ snp.allele = snp.allele,
> snpfirstdim=TRUE)Error in snpgdsCreateGeno(filn, genmat = genod, sample.id =
> sample.id, :
is.matrix(genmat) is not TRUE
Thanks,
Meriam
On Tue, Jan 8, 2019 at 9:02 AM PIKAL Petr <petr.pi...@precheza.cz> wrote:
> 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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--
*Meriam Nefzaoui*
*MSc. in Plant Breeding and Genetics*
*Universidade Federal Rural de Pernambuco (UFRPE) - Recife, Brazil*
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