conStruct analysis

[AnjumanArif]

can not understand what is this error while running conStruct."Error in if (any(args[["geoDist"]] < 0)) { : missing value where TRUE/FALSE needed".** I have checked everything is fine. Please help

[petrelharp]

Sorry to hear that you are having difficulties! To help debug your problem, could you please post the code you are running to produce the error, and at least a description of the input files?

[AnjumanArif]

Hi, Thanks for replying. I have 192 genotypes with 12763 loci in construct file. I am using these commands as below for data construction and attaching the longitude and latitude file (coord) and out file (geoDist) in excel fomat after copying from RStudio. : Also attaching a subset of structure text file of all SNPs. x<-as.numeric(c(142.702789,--------------------)) length(x) 192 long<-x x<-as.numeric(c(-20.917574,)) length(x) lati<-x coord<-cbind(long,lati) is.matrix(coord)

alleleFreq matrix----

output file freqs used for analysis as such after structure2conStruct formatting.

geoMatrix

fields::rdist.earth(x1 = coord,x2 = NULL, miles = TRUE, R = NULL) out<- rdist.earth (coord) upper<- col(out)> row( out) hist( out[upper]) geoDist<-out

conStruct analysis----

data(anjumConStruct)

anjumConStruct <- list(freqs=freqs, coord=coord, geoDist=geoDist)

my.run<- conStruct(spatial = TRUE, K = 3, freqs = anjumConStruct$freqs, geoDist = anjumConStruct$geoDist, coords = anjumConStruct$coord, prefix = "spK3", n.chains = 1, n.iter = 1000, make.figs = TRUE, save.files = TRUE)

my.run <- conStruct(spatial = TRUE, K = 3, freqs = anjumconStruct$freqs, geoDist = anjumconStruct$geoDist, coords = anjumconStruct$coord, prefix = "spK") I am recieving this error as below: Error in if (any(args[["geoDist"]] < 0)) { : missing value where TRUE/FALSE needed

I will cordially appreciate your help. Thanks and stay blessed Anjum

On Thu, Oct 31, 2019 at 9:11 PM Peter Ralph notifications@github.com wrote:

Sorry to hear that you are having difficulties! To help debug your problem, could you please post the code you are running to produce the error, and at least a description of the input files?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/gbradburd/conStruct/issues/27?email_source=notifications&email_token=AMOFTPBMKSZ4SIRLKGHFPMLQRL7SXA5CNFSM4JHIAKP2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOECYLE4Y#issuecomment-548450931, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMOFTPFHTCE66YRU7TLJ2MDQRL7SXANCNFSM4JHIAKPQ .

[AnjumanArif]

Hi, I have resolved the issue for this part. If required will get back for assistance.

[AnjumanArif]

thanks a lot.