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/
