在R中组合多个控制流语句时出错？

Question

我正在努力将R中的多个条件组合起来。我能够使它适用于单个条件但我不断遇到多个条件错误。这是一个例子..

#!/usr/bin/Rscript
    library(getopt)
    args<-commandArgs(TRUE)    
    options<-matrix(c('lincRNA',    'l',    1,  "character",
                          'lincRNAbed', 'b',    1,  "character",
                          'overlap',    'v',    2,  "character",
                          'tss',        't',    2,  "character",
                          'help',       'h',    0,  "logical"),
                           ncol=4,byrow=TRUE)

ret.opts<-getopt(options,args)

# No TSS file here
if(is.null(ret.opts$tss)) {
    # All lincRNA's
    fastaFile <- readDNAStringSet(ret.opts$lincRNA)
    lincRNA_ID = names(fastaFile)
    sequence = paste(fastaFile)
    size = width(fastaFile)
    df <- data.frame(lincRNA_ID, size)
# No overlap file here
} else if(is.null(ret.opts$overlap)) {
    # All lincRNA's
    fastaFile <- readDNAStringSet(ret.opts$lincRNA)
    lincRNA_ID = names(fastaFile)
    sequence = paste(fastaFile)
    size = width(fastaFile)
    df <- data.frame(lincRNA_ID, size)
# Both not present
} else if(is.null(ret.opts$tss) && is.null(ret.opts$overlap)){
  # All lincRNA's
  fastaFile <- readDNAStringSet(ret.opts$lincRNA)
  lincRNA_ID = names(fastaFile)
  sequence = paste(fastaFile)
  size = width(fastaFile)
  df <- data.frame(lincRNA_ID, size)
# Both present
} else {
    # All lincRNA's
    fastaFile <- readDNAStringSet(ret.opts$lincRNA)
    lincRNA_ID = names(fastaFile)
    sequence = paste(fastaFile)
    size = width(fastaFile)
    df <- data.frame(lincRNA_ID, size)
}

适用于条件1,2和4.这是一个例子

Rscript test.R --lincRNA lincRNAs.fa --lincRNAbed lincRNAs.bed --tss lincRNAs.with.CAGE.support.annotated.fa
Rscript test.R --lincRNA lincRNAs.fa --lincRNAbed lincRNAs.bed --overlap lincRNAs.overlapping.known.lincs.fa
Rscript test.R --lincRNA lincRNAs.fa --lincRNAbed lincRNAs.bed --overlap lincRNAs.overlapping.known.lincs.fa --tss lincRNAs.with.CAGE.support.annotated.fa 

但是当我用多个条件运行它时，我不断收到错误。

Rscript test.R --lincRNA lincRNAs.fa --lincRNAbed lincRNAs.bed
Error in .normarg_input_filepath(filepath) : 
              'filepath' must be a character vector with no NAs
            Calls: readDNAStringSet ... fasta.index -> <Anonymous> -> .normarg_input_filepath
            Execution halted

我知道多个条件的语法是错误的，但我无法弄清楚它是什么。我尝试了不同的方法但没有成功。