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 <- 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.pikal at precheza.cz> wrote:

Hi

see in line

-----Original Message-----
From: R-help <r-help-bounces at r-project.org> On Behalf Of N Meriam
Sent: Tuesday, January 8, 2019 3:08 PM
To: r-help at 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

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