Question: Gapit tool error
0
gravatar for mmh7272
2.1 years ago by
mmh727250
mmh727250 wrote:

Hi fellow happy new year i am a student who just have studied bioinfomatics. so i have problem. i use Gapit tool pupose of GWAS. i have phenotype data.txt and snp.hp file so i use gapit tool this is script when i use in R

===================================================
library('MASS')
library(multtest)
library(genetics)
library(gplots)
library(compiler)
library("scatterplot3d")
myY <- read.table("/home/mmh7272/cp/t18/sand1.txt", head=T)
source("/home/mmh7272/gapit/gapit.txt")
source("/home/mmh7272/gapit/gapit_functions_MLM.txt")
myG <- read.table("/home/mmh7272/cp/292.snp.out.hp", head=F)
myG <-myG[,c(1:11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303)]
source("/home/mmh7272/gapit/gapit.txt")
source("/home/mmh7272/gapit/gapit_functions_MLM.txt")
GAPIT <- GAPIT(Y=myY, G=myG, PCA.total=3, SNP.MAF=0.05, Model.selection=TRUE)
==================================================================
it happens error

[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"
  Error in aperm.default(X, c(s.call, s.ans)) :
  long vectors not supported yet: /builddir/patched_source/src/main/memory.c:1668**
In addition: Warning messages:
1: 'memory.size()' is Windows-specific
2: 'memory.size()' is Windows-specific
3: 'memory.size()' is Windows-specific
4: 'memory.size()' is Windows-specific

i dont know solution plz help me

snp R • 1.0k views
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by mmh727250

Thanks for the great answer. Can u tell me how to fix?

ADD REPLYlink written 2.1 years ago by mmh727250

use a smaller dataset.

ADD REPLYlink written 2.1 years ago by Pierre Lindenbaum125k

ok i try thanks you

ADD REPLYlink written 2.1 years ago by mmh727250

happy new year ! i reduce a smaller dataset as ur tip so i have another error

Error in if(bit == 1) { : missing value where TRUE/FALSE needed

what's poroblem?

ADD REPLYlink written 2.1 years ago by mmh727250

update R to version > 3.0

ADD REPLYlink written 2.1 years ago by Santosh Anand5.0k

thanks u for ur tip i complete.!

ADD REPLYlink written 2.1 years ago by mmh727250

If it did work, please close this thread.

ADD REPLYlink written 2.0 years ago by Santosh Anand5.0k
1
gravatar for Pierre Lindenbaum
2.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum125k wrote:

you dataset is too large for this R library. see https://stackoverflow.com/questions/24335692/

ADD COMMENTlink written 2.1 years ago by Pierre Lindenbaum125k
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