[R] Warning message: NAs introduced by coercion
PIKAL Petr
petr@pik@l @ending from prechez@@cz
Wed Jan 9 10:03:34 CET 2019
And as you use bioconductor related package you probably could get better answers in specialised biconductor help
https://www.bioconductor.org/help/
Cheers
Petr
From: N Meriam <meriam.nef using gmail.com>
Sent: Tuesday, January 8, 2019 4:36 PM
To: PIKAL Petr <petr.pikal using precheza.cz>
Cc: r-help using r-project.org
Subject: Re: [R] Warning message: NAs introduced by coercion
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<http://sample.id> <- names(myd)[-1]
> snp.id<http://snp.id> <- myd[,1]
> snp.position <- 1:length(snp.id<http://snp.id>) # not needed for ibs
> snp.chromosome <- rep(1, each=length(snp.id<http://snp.id>)) # not needed for ibs
> snp.allele <- rep("A/G", length(snp.id<http://snp.id>)) # not needed for ibs
> # genotype data must have - in 3
> genod <- myd[,-1]
> genod[is.na<http://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<http://sample.id> = sample.id<http://sample.id>, snp.id<http://snp.id> = snp.id<http://snp.id>,
+ snp.chromosome = snp.chromosome,
+ snp.position = snp.position,
+ snp.allele = snp.allele, snpfirstdim=TRUE)
Error in snpgdsCreateGeno(filn, genmat = genod, sample.id<http://sample.id> = sample.id<http://sample.id>, :
is.matrix(genmat) is not TRUE
Thanks,
Meriam
On Tue, Jan 8, 2019 at 9:02 AM PIKAL Petr <petr.pikal using precheza.cz<mailto:petr.pikal using precheza.cz>> wrote:
Hi
see in line
> -----Original Message-----
> From: R-help <r-help-bounces using r-project.org<mailto: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<mailto: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<http://sample.id> <- names(myd)[-1]
> > snp.id<http://snp.id> <- myd[,1]
> > snp.position <- 1:length(snp.id<http://snp.id>) # not needed for ibs
> > snp.chromosome <- rep(1, each=length(snp.id<http://snp.id>)) # not needed for ibs
> > snp.allele <- rep("A/G", length(snp.id<http://snp.id>)) # not needed for ibs
> # genotype data must have - in 3
> > genod <- myd[,-1]
> > genod[is.na<http://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
>
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>
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Meriam Nefzaoui
MSc. in Plant Breeding and Genetics
Universidade Federal Rural de Pernambuco (UFRPE) - Recife, Brazil
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