RunMHCAlleles: RunMHCAlleles

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

Description

Run a ALL the available MHCI peptides or by specie (This function is called by RunAllMHC)

Usage

RunMHCAlleles(
  seqfile,
  alleleList,
  rthParam = 0.5,
  rltParam = 2,
  tParam = -99.9002,
  nCores
)

Arguments

seqfile	character with the file path of the fasta file (it should be .fasta and contain onle 1 sequence, Multifasta files in progress)
alleleList	a list of characters containing alleles list(l1 = c("HLA-A01:01","HLA-A02:01"), l2 = c("HLA-A26:01","HLA-B08:01"))
rthParam	float (default 0.5) upper limit for strong binder (SB -> peptide percentage rank < rhtParam)
tParam	tparam
nCores	integer indicating the number of used CPUs or workers from BiocParallele
rlhParam	float (default 2.0) upper limit for weak binder WB -> rhtParam <= peptide percentrank < rltParam

Details

run netMHCIIpan trhough the sequence fasta file for each MHCII Allele

Value

a character

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