Warning message: NAs introduced by coercion

Yes, sorry. I attached the file once again.
Well, still getting the same warning.
class(genod) <- "numeric"
Warning message:
In class(genod) <- "numeric" : NAs introduced by coercion
class(genod)
[1] "matrix"

Then, I run the following code and it gives this:
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)
# calculate similarity matrix
# Open the GDS file
(genofile <- snpgdsOpen(filn))
File: C:\Users\DELL\Documents\TEST\simTunesian.gds (1.4M)
+    [  ] *
|--+ sample.id   { Str8 363 ZIP_ra(42.5%), 755B }
|--+ snp.id   { Int32 15752 ZIP_ra(35.1%), 21.6K }
|--+ snp.position   { Int32 15752 ZIP_ra(34.7%), 21.3K }
|--+ snp.chromosome   { Float64 15752 ZIP_ra(0.18%), 230B }
|--+ snp.allele   { Str8 15752 ZIP_ra(0.16%), 108B }
\--+ genotype   { Bit2 15752x363, 1.4M } *
ibs <- snpgdsIBS(genofile, remove.monosnp = FALSE, num.thread=1)
Identity-By-State (IBS) analysis on genotypes:
Excluding 0 SNP on non-autosomes
Working space: 363 samples, 15,752 SNPs
    using 1 (CPU) core
IBS:    the sum of all selected genotypes (0,1,2) = 3658952
Tue Jan 08 15:38:00 2019    (internal increment: 42880)
[==================================================] 100%, completed in 0s
Tue Jan 08 15:38:00 2019    Done.
# maximum similarity value
max(ibs$ibs)
[1] NaN
# minimum similarity value
min(ibs$ibs)
[1] NaN

As you can see, I can't continue my analysis (heat map plot,
clustering with hclust) because values are NaN.
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-bounces at r-project.org] On Behalf Of N Meriam
Sent: Tuesday, January 8, 2019 1:38 PM
To: Michael Dewey <lists at dewey.myzen.co.uk>
Cc: r-help at 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 <lists at 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.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

[[alternative HTML version deleted]]

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http://www.dewey.myzen.co.uk/home.html

--
Meriam Nefzaoui
MSc. in Plant Breeding and Genetics
Universidade Federal Rural de Pernambuco (UFRPE) - Recife, Brazil

Meriam Nefzaoui
MSc. in Plant Breeding and Genetics
Universidade Federal Rural de Pernambuco (UFRPE) - Recife, Brazil

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