Description Usage Arguments Details Value Examples
call_gt
calls transcribed genotypes using allele RNA-seq read counts
1 | call_gt(acset, min_acount = 3, fc = 3)
|
acset |
An acset list created by the function |
min_acount |
An integer specifying the minimum number of reads required to be present for at least one of the two alleles as to make a call. If not fulfilled the call is set to NA. |
fc |
An integer specifying the fold-change cutoff between the expression of the alternative and reference allele (fc.observed = alternative allele count / reference allele count). The transcribed genotype call is set to 0 if fc.observed <= fc, 2 if fc.observed >= fc and 1 otherwise (if there are enough reads present, see the "min_acount" parameter). |
This is a simplistic transcribed genotype caller which is used to discretize which allele is the most expressed. For each variant and cell one of four possible discrete values is set depending on the expression of the two alleles. 0: reference allele most highly expressed, 1: bi-allelic expression with similar degree of expression from the two alleles, 2: alternative allele most highly expressed, or, NA if there are not enough reads to make a call.
acset An acset list where the "gt" element is set or updated. "gt" is a matrix with integer values representing transcribed genotype calls. 0: reference allele most highly expressed, 1: bi-allelic expression with similar degree of expression from the two alleles, 2: alternative allele most highly expressed. NA's are used to represent entries where no call could be made. The rownames are set to the variant column, "var", of featdata. The colnames are set to the colnames of "refcount". The elements [['args']][['filter']][c('min_acount', 'fc')] are added or updated to the acset as to record the filter arguments used.
1 2 3 4 5 6 7 8 9 10 |
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.