[R] Warning message: NAs introduced by coercion

PIKAL Petr petr@pik@l @ending from prechez@@cz
Wed Jan 9 09:57:38 CET 2019


Hm,

you should use dput for sharing data but my suggestion was correct.

You converted genod to genod2 by as.matrix what changed it to „character“ matrix as matrix is able to hold only one type of data. By trying to change it to numeric, all numbers are changed to numeric and what cannot be changed is simply converted to NA (with polite warning).

You should read documentation to
snpgdsCreateGeno
as it requires matrix as an input and maybe also pay attention to the basic documents like R-intro which would teach you difference between matrix and data frame (chapter 3).

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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