R/check_extras.R

In mikelove/polyesterAlpineMs: Simulate RNA-seq reads

# function to make sure everything is compatible and assign sane defaults
# internal

.check_extras = function(extras, paired){

    if(!('distr' %in% names(extras))){
        extras$distr = 'normal'
    }else{
        extras$distr = match.arg(extras$distr, 
            c('normal', 'empirical', 'custom'))
        if(extras$distr == 'custom' & !('custdens' %in% names(extras))){
            stop(.makepretty('to use custom fragment distribution, provide
                "custdens", a logspline object representing the distribution.'))
        }
    }
    if(!('fraglen' %in% names(extras))){
        extras$fraglen = 250
    }
    if(!('fragsd' %in% names(extras))){
        extras$fragsd = 25
    }## I don't love this--these arguments aren't needed unless distr is normal.
    # but we store them anyway. should code better?
    if(!('readlen' %in% names(extras))){
        extras$readlen = 100
    }

    if(!('bias' %in% names(extras))){
        extras$bias = 'none'
    }else{
        extras$bias = match.arg(extras$bias, c('none', 'rnaf', 'cdnaf'))
    }

    if(!('error_model' %in% names(extras))){
        extras$error_model = 'uniform'
    }
    .check_error_model(extras, paired)

    if(!('error_rate' %in% names(extras))){
        extras$error_rate = 0.005
    }
    if(extras$error_model == 'custom'){
        extras$path = paste0(extras$model_path, '/', extras$model_prefix)
    }#this should work beause we already checked stuff.

    if(!('bias' %in% names(extras))){
        extras$bias = 'none'
    }else{
        extras$bias = match.arg(extras$bias, c('none', 'rnaf', 'cdnaf'))
    }

    return(extras)

}