r - 将shell变量导入R

Question

我是 R 的初学者

我不知道如何将我的 shell 变量导入 R。

read -p " enter the Read :" r1

tabix -h -R Reference/Covered_region.bed output/"$r1"/"$r1".vcf.gz > output/"$r1"/Covered_"$r1".vcf

perl convert2annovar.pl -format vcf4 output/"$r1"/Covered_"$r1".vcf -outfile output/"$r1"/Covered_"$r1".avinput -includeinfo -withzyg

perl table_annovar.pl output/"$r1"/Covered_"$r1".avinput humandb/ -buildver hg38 -out output/"$r1"/"$r1"_GATK.hg38_multianno.csv -csvout

现在我想将我的 perl 脚本output/"$r1"/"$r1"_GATK.hg38_multianno.csv的最后一个输出导入 R

我的 R 脚本看起来像

library(readr)

test <- read_csv("/output/"$r1"/"$r1"_GATK.hg38_multianno.csv")
data= test[!duplicated(as.list(test))]
filtering= data[data$`1000g2015aug_all` <=0.01,]
write.csv(data,"output/"$r1"/"$r1".csv",row.names = F)

标签： rshell

Answer 1

library(readr)

#importing data

args <- commandArgs(TRUE)

filename <-args[1]

filename1 <-args[2]

testdata <- read_csv(filename)

data= testdata[!duplicated(as.list(testdata))]

filtering= data[data$`1000g2015aug_all` <=0.01,]

write.csv(data,paste0(filename1,".csv"),row.names = F)

使用 Rscript Filtering_variants.r test1.csv out 2>out_error.txt