RunMHCIIAlleles: RunMHCIIAlleles

In elmerfer/RAPInetMHCpan: an R API to netMHCpan and netMHCIIpan softwares for neural network prediction of peptide binders

Description

Run a peptides between 8 to 14 mers along a fasta sequence (from file)

Usage

RunMHCIIAlleles(
  seqfile,
  alleleList,
  rankS = 0.5,
  rankW = 10,
  rankF = rankW,
  pepLength = 15,
  nCores
)

Arguments

seqfile	character with the file path of the fasta file (it should be .fasta and contain onle 1 sequence)
alleleList	a character vector with the MHCII allele sequences c("DRB1_0101") or c("DRB1_0101","DRB1_0111") and so on. If NULL it will be automatically downloaded from the netMHCIIpan server (it may take time)
rankS	float (default 0.5) upper limit for strong binder
rankW	float (default 10.0) upper limit for weak binder
rankF	float (default 10.0) filter to show peptide binders
pepLength	integer (default 15) length of the tested peptide
nCores	number of used CPS or worker for BiocParallel

Details

run netMHCIIpan trhough the sequence fasta file for each MHCII Allele

Value

a data.frame

elmerfer/RAPInetMHCpan documentation built on Sept. 17, 2021, 2:14 p.m.