[R] Warning message: NAs introduced by coercion
Michael Dewey
li@t@ @ending from dewey@myzen@co@uk
Tue Jan 8 18:28:35 CET 2019
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 using precheza.cz> wrote:
>
>> Hi
>>
>> see in line
>>
>>> -----Original Message-----
>>> From: R-help <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
>>> 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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--
Michael
http://www.dewey.myzen.co.uk/home.html
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