在R中运行Shell命令脚本（Call shell commands from R）

aaa.R
Args <- commandArgs()
cat("Args[1]=",Args[1],"\n")
cat("Args[2]=",Args[1],"\n")
cat("Args[3]=",Args[3],"\n")
cat("Args[4]=",Args[4],"\n")
cat("Args[5]=",Args[5],"\n")
cat("Args[6]=",Args[6],"\n")

shell_cmd<-paste0("grep -n CHR ",Args[6])
grep_out<-system(shell_cmd, intern = TRUE)
cat(grep_out)

how to run:

/myPathToRscript/Rscript aaa.R  bbb.vcf

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Description

system invokes the OS command specified by command.

Usage

system(command, intern = FALSE,
       ignore.stdout = FALSE, ignore.stderr = FALSE,
       wait = TRUE, input = NULL, show.output.on.console = TRUE,
       minimized = FALSE, invisible = TRUE)

Arguments

command	the system command to be invoked, as a character string.
intern	a logical (not NA) which indicates whether to capture the output of the command as an R character vector.
ignore.stdout, ignore.stderr	a logical (not NA) indicating whether messages written to ‘stdout’ or ‘stderr’ should be ignored.
wait	a logical (not NA) indicating whether the R interpreter should wait for the command to finish, or run it asynchronously. This will be ignored (and the interpreter will always wait) if intern = TRUE.
input	if a character vector is supplied, this is copied one string per line to a temporary file, and the standard input of command is redirected to the file.
show.output.on.console, minimized, invisible	arguments that are accepted on Windows but ignored on this platform, with a warning.

=============================================

Invoke a System Command, using a Shell

Description

shell runs the command specified by cmd, usually under a shell.

Usage

shell(cmd, shell, flag="/c", intern=FALSE, wait=TRUE,
      translate=FALSE, mustWork=FALSE, ...)

Arguments

cmd	the system command to be invoked, as a string.
shell	a string giving the name of the shell to be used, or NULL (no shell). If missing, a suitable shell is chosen: see ‘Details’.
flag	the switch to run a command under the shell. If the shell is bash or tcsh the default is changed to "-c".
intern	a logical, indicates whether to make the output of the command an R object.
wait	should the R interpreter wait for the command to finish? The default is to wait, and the interpreter will always wait if intern = TRUE.
translate	If TRUE, "/" in cmd is translated to "\".
mustWork	a logical; if TRUE failure to run the command will give an R error.

REF:

http://astrostatistics.psu.edu/datasets/R/html/base/html/shell.html

https://stat.ethz.ch/R-manual/R-devel/library/base/html/system.html