在非Linux系统的电脑也可以使用命令行工具操作R语言

>  R.home()
[1] "/Library/Frameworks/R.framework/Resources"
> 

ls -lh /Library/Frameworks/R.framework/Resources/bin/|cut -d " " -f 7-

  1.8K Apr  1 10:39 BATCH
  2.1K Apr  1 10:39 COMPILE
  825B Apr  1 10:39 INSTALL
  1.3K Apr  1 10:39 LINK
  8.9K Apr  1 10:39 R
  160B Apr  1 10:39 REMOVE
  1.4K Apr  1 10:39 Rcmd
  318B Apr  1 10:39 Rd2pdf
  361B Apr  1 10:39 Rdconv
  260B Apr  1 10:39 Rdiff
  312B Apr  1 10:39 Rprof
   53K Apr  1 10:41 Rscript
  157B Apr  1 10:39 SHLIB
  320B Apr  1 10:39 Stangle
  318B Apr  1 10:39 Sweave
  352B Apr  1 10:39 build
  319B Apr  1 10:39 check
   12K Apr  1 10:39 config
   96B Apr  1 10:41 exec
  2.9M Apr  1 10:41 fc-cache
   14K Apr  1 10:39 javareconf
  342K Apr  1 10:39 libtool
  3.4K Apr  1 10:39 mkinstalldirs
  481B Apr  1 10:39 pager
  2.3M Apr  1 10:41 qpdf
  4.0K Apr  1 10:39 rtags

alias R='/Library/Frameworks/R.framework/Resources/bin/R'
alias Rscript='/Library/Frameworks/R.framework/Resources/bin/Rscript'

(base) jmzeng@jmzengs-iMac peaks_anno % R

R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 

t1<-Sys.time()
temp_args <- commandArgs(trailingOnly = T)

if(length(temp_args) != 3){
  cat("运行命令方式：Rscript test.R folder sample species \n")
  quit("no")
}else{
  bedPeaksFile <- temp_args[1]
  species <-temp_args[2]
  folder <-temp_args[3]
  #BiocManager::install(c('ChIPseeker','TxDb.Hsapiens.UCSC.hg38.knownGene','org.Hs.eg.db'))
  # BiocManager::install("TxDb.Mmusculus.UCSC.mm10.knownGene")
  # BiocManager::install("ChIPseeker")
  require(ChIPseeker)
  require(TxDb.Hsapiens.UCSC.hg38.knownGene)
  require(TxDb.Mmusculus.UCSC.mm10.knownGene) 
  require(org.Hs.eg.db) 
  require(org.Mm.eg.db) 
  
  bedPeaksFile 
  cat(paste0('Now we process ', bedPeaksFile  ))
  peak <- readPeakFile( bedPeaksFile )  
  # table(seqlevels(peak))
  # keepChr= !grepl('_',seqlevels(peak))
  # seqlevels(peak, pruning.mode="coarse") <- seqlevels(peak)[keepChr]
  # table(seqlevels(peak))
  cat(paste0('there are ',length(peak),' peaks for this data' ))
  
  if(species=='human'){
    txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene 
    peakAnno <- annotatePeak(peak, tssRegion=c(-3000, 3000), 
                             TxDb=txdb, annoDb="org.Hs.eg.db") 
  }else{
    txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene 
    peakAnno <- annotatePeak(peak, tssRegion=c(-3000, 3000), 
                             TxDb=txdb, annoDb="org.Mm.eg.db") 
  }
  
  df=as.data.frame(peakAnno)
  cg_df = df[,c(1,2,4,23)]
  head(cg_df)
  cl=ifelse(grepl('Promoter',df$annotation),'Promoter',
            ifelse(grepl('Intron',df$annotation),'Intron',
                   ifelse(grepl('Intergenic',df$annotation),'Intergenic',
                          ifelse(grepl('Exon',df$annotation),'Exon',
                                 'other'))))
  table(cl)
  cg_df$anno=cl
  plotAnnoPie(peakAnno)
  write.table(cg_df,sep = '\t',quote = F,row.names = F,col.names = F,
              file = file.path(folder,
                               gsub('sort_peaks.narrowPeak.bed','ChIPseeker_anno.txt',
                                    basename(bedPeaksFile))))
  
  print("all done!!!")
  t2<-Sys.time()
  t2
  df <- t1-t2
  print(df)
} 

 Rscript anno.R  sort_peaks.narrowPeak.bed  human tf_human/