pass user arg to DESeq2 function
arguments, bioconductor, optparse, r, string-parsing
Solution
I think you need `as.formula(opt$design)`.
x <- "~taxonomy"
f <- ~taxonomy
str(f)
## Class 'formula' language ~taxonomy
## ..- attr(*, ".Environment")=<environment: R_GlobalEnv>
identical(f,as.formula(x)) ## TRUE
Problem
I'm trying to run `DESeq` in an RScript using parameters input from the command line. I used `optparse` to parse user arguments and am trying to pass the design argument into the `DESeqDataSetFromMatrix()` function. I tested the function directly and it works perfectly: ``` DESeq_tbl <- DESeqDataSetFromMatrix(countData=counts_tbl, colData=coldata, design=~taxonomy) ``` However, if I try to pass the variable `opt$design` (which is a character string = "~taxonomy"), I get the following error: ``` DESeq_tbl <- DESeqDataSetFromMatrix(countData=counts_tbl, colData=coldata, design=opt$design) ``` Error: $ operator is invalid for atomic vectors Execution halted I've tried `noquote()`, various combinations of `cat`/`paste` and creating the entire command as a string to pass to the `DESeqDataSetFromMatrix()` function, but nothing has worked. Any advice would be greatly appreciated. the solution Thanks to Ben Bolker's answer below, the following worked: ``` DESeq_tbl <- DESeqDataSetFromMatrix(countData=counts_tbl, colData=coldata, design=as.formula(opt$design)) ```