Here's a portion of what my data looks like (text file format attached).
When running in R, it gives me this:
> 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
Can't find a solution to my problem...my guess is that the problem
comes from converting the column 'marker' factor to numerical.
Best,
Meriam
On Tue, Jan 8, 2019 at 11:28 AM Michael Dewey <li...@dewey.myzen.co.uk> wrote:
>
> Dear Meriam
>
> Your csv file did not come through as attachments are stripped unless of
> certain types and you post is very hard to read since you are posting in
> HTML. Try renaming the file to ????.txt and set your mailer to send
> plain text then people may be able to help you better.
>
> Michael
>
> On 08/01/2019 15:35, N Meriam wrote:
> > 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]]
> >>>
> >>> ______________________________________________
> >>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> >>> https://stat.ethz.ch/mailman/listinfo/r-help
> >>> PLEASE do read the posting guide
> >> http://www.R-project.org/posting-guide.html
> >>> and provide commented, minimal, self-contained, reproducible code.
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> >
>
> --
> Michael
> http://www.dewey.myzen.co.uk/home.html
--
Meriam Nefzaoui
MSc. in Plant Breeding and Genetics
Universidade Federal Rural de Pernambuco (UFRPE) - Recife, Brazil
marker X88 X9 X17 X25
3 100023173|F|0-47:G>A-47:G>A 0 NA NA NA
4 1043336|F|0-7:A>G-7:A>G 1 0 NA 0
5 1212218|F|0-49:A>G-49:A>G 0 0 0 0
6 1019554|F|0-14:T>C-14:T>C 0 0 NA 0
8 100024550|F|0-16:G>A-16:G>A NA NA NA NA
10 1106702|F|0-8:C>A-8:C>A 0 0 0 0
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