Question: Gapit error for gwas
0
gravatar for mmh7272
15 months ago by
mmh727250
mmh727250 wrote:

I am using GAPIT package in R for GWAS. Some data can not work. And the output is given below: There is an Error in crossprod(x, y) : requires numeric/complex matrix/vector arguments In addition: There were 36 warnings (use warnings() to see them) . So, how to solve this problem?

[1] "--------------------- Welcome to GAPIT ----------------------------" [1] "Genotyping: numericalization, sampling kinship, PCs and much more..." [1] "Converting genotype..." [1] "Converting HapMap format to numerical under model of Middle" [1] "Perform numericalization" [1] "Succesfuly finished converting HapMap which has bits of 2" [1] "Converting genotype done." [1] "Callingg prcomp..." [1] "Creating PCA graphs..." [1] "Joining taxa..." [1] "Exporting PCs..." [1] "PC created" [1] "Calculating kinship..." [1] "Number of individuals and SNPs are 276 and 854552" [1] "Calculating kinship with VanRaden method..." [1] "Getting X'X..." [1] "Adjusting..." [1] "Calculating kinship with VanRaden method: done" [1] "kinship calculated" [1] "Creating heat map for kinship..." [1] "Kinship heat map created" [1] "Adding IDs to kinship..." [1] "Writing kinship to file..." [1] "Kinship save as file" [1] "Kinship created!" [1] "--------------------Processing traits----------------------------------" [1] "Phenotype provided!" [1] "Processing trait: X1" [1] "------------Examining data (QC)------------------------------------------" [1] "QC is in process..." [1] "Removing duplicates..." [1] "Removing NaN..." [1] "Remove duplicates for GT..." [1] "Remove duplicates for KI..." [1] "Remove duplicates for Z (column wise)..." [1] "Maching Z with Kinship colwise..." [1] "Maching Z without origin..." [1] "Maching GT and CV..." [1] "QC final process..." [1] "size of taxa.kept" [1] 276 1 [1] "GAPIT.QC accomplished successfully!" [1] "The value of QC is" [1] TRUE [1] "Try to group from and to were set to 1" [1] "------------Examining data (QC) done-------------------------------------" [1] "-------------------Sandwich burger and dressing------------------------" [1] "-------------------------Iteration in process--------------------------" [1] "Total iterations: 25" [1] "-------Mixed model with Kinship-----------------------------" Error in crossprod(x, y) : requires numeric/complex matrix/vector arguments In addition: There were 36 warnings (use warnings() to see them)

warning function (..., call. = TRUE, immediate. = FALSE, noBreaks. = FALSE, domain = NULL) { args <- list(...) if (length(args) == 1L && inherits(args[[1L]], "condition")) { cond <- args[[1L]] if (nargs() > 1L) cat(gettext("additional arguments ignored in warning()"), "\n", sep = "", file = stderr()) message <- conditionMessage(cond) call <- conditionCall(cond) withRestarts({ .Internal(.signalCondition(cond, message, call)) .Internal(.dfltWarn(message, call)) }, muffleWarning = function() NULL) invisible(message) } else .Internal(warning(call., immediate., noBreaks., .makeMessage(..., domain = domain))) } <bytecode: 0x6706fb08=""> <environment: namespace:base="">

snp R software error • 661 views
ADD COMMENTlink written 15 months ago by mmh727250
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