Cleaning data (Quality control)


#1

Hello Sir,
I want to clean the whole genome sequencing data for African sheep. I used Rstudio version R643.4.2. I have followed the steps below:
####Quality control for African sheep
####ICARDA,ILRI,Addis
####27.11.2017

####Set working directory
setwd(“F:/Kareem/sheep”)
####Read data which are stored in text format
infile-<-“Africa"
command<-“plink–sheep–nonfounders–allow-no-sex"
command<-paste(command,”–file”,infile,"–make-bed–out",infile)
system(command)

but if i run system command it gives me message error as follows:
setwd(“F:/Sheep”)

command<-“plink–sheep–nonfounders–allow-no-sex"
command<-paste(command,”–file",infile,"–make-bed–out",infile)
Error in paste(command, “–file”, infile, “–make-bed–out”, infile) :
object ‘infile’ not found
system(command)
Warning message:
running command ‘plink–sheep–nonfounders–allow-no-sex’ had status 127
what i can do? my laptop is 64 bit, windows 7, office 2007
Please help me
Thank you


#2

infile-<-“Africa"

I think you may have a typo in your declaration for infile. Try removing the dash after the e so it just becomes:

infile <- "Africa"