RunAllMHC: RunAllMHC

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

Usage

RunAllMHC(
  seqfile,
  alleleGroup = c("HLA", "BoLA", "Gogo", "H", "H2", "Mamu", "Patr", "SLA", "All"),
  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)
alleleGroup	a character vector indicating whi allele family, possible values are "HLA","BoLA", "Gogo","H","H2", "Mamu", "Patr","SLA", "All"
rthParam	float (default 0.5) upper limit for strong binder (SB -> peptide percent rank < rhtParam)
tParam	tparam
nCores	integer indicating the number of used CPUs or workers (see BiocParallele)
rlhParam	float (default 2.0) upper limit for weak binder (WB -> rhtParam <= peptide percent rank < 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.