Your attached file is not a .csv file since the field are not separated by commas (just rename the mydata.csv to mydata.txt).
The command "genod2 <- as.matrix(genod)" created a character matrix from the data frame genod. When you try to force genod2 to numeric, the marker column becomes NAs which is probably not what you want. The error message is because you passed genod (a data frame) to the snpgdsCreateGeno() function not genod2 (the matrix you created from genod). ------------------------------------ David L. Carlson Department of Anthropology Texas A&M University -----Original Message----- From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of N Meriam Sent: Tuesday, January 8, 2019 1:38 PM To: Michael Dewey <li...@dewey.myzen.co.uk> Cc: r-help@r-project.org Subject: Re: [R] Warning message: NAs introduced by coercion 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. > >> Osobní údaje: Informace o zpracování a ochraně osobních údajů obchodních > >> partnerů PRECHEZA a.s. jsou zveřejněny na: > >> https://www.precheza.cz/zasady-ochrany-osobnich-udaju/ | Information > >> about processing and protection of business partner’s personal data are > >> available on website: > >> https://www.precheza.cz/en/personal-data-protection-principles/ > >> Důvěrnost: Tento e-mail a jakékoliv k němu připojené dokumenty jsou > >> důvěrné a podléhají tomuto právně závaznému prohláąení o vyloučení > >> odpovědnosti: https://www.precheza.cz/01-dovetek/ | This email and any > >> documents attached to it may be confidential and are subject to the legally > >> binding disclaimer: https://www.precheza.cz/en/01-disclaimer/ > >> > >> > > > > -- > 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 ______________________________________________ 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.
