mercredi 21 septembre 2016

Error in combining multiple conditionals in R?

I am struggling with combining multiple conditionals in R. I was able to make it work for the single conditional but i keep getting error with multiple conditionals. Here is a example..

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)

My R script is something like this

if(is.null(ret.opts$tss)) {
 -------------------------
} else if(is.null(ret.opts$overlap)) {
 -------------------------
} else if(is.null(ret.opts$tss) && is.null(ret.opts$overlap)){
 -------------------------
}

But when run it with single conditional it works but i when run multiple conditional, i keep getting error

Rscript ../../final_summary_table_gen_evo-I.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

I know the syntax for multiple conditionals is wrong but i can't figure out what it is. I tried different ways but without success.

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