RunNetMHCPan: RunNetMHCPan

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

RunNetMHCPan(
  seqfile,
  allele,
  rthParam = 0.5,
  rltParam = 2,
  tParam = -99.9002,
  pLength
)

Arguments

seqfile	character with the file path of the fasta file (it should be .fasta and contain onle 1 sequence)
allele	a character vector with the HLA sequences c("HLA-A01:01") or c("HLA-A01:01","HLA-A02:01") and so on. If NULL it will be automatically downloaded from the netMHCpan server (it may take time)
rthParam	float (default 0.5) upper limit for strong binder (SB -> peptide percent rank < rhtParam)
tParam	tparam
rlhParam	float (default 2.0) upper limit for weak binder (WB -> rhtParam <= peptide percent rank < rltParam )

Details

run netMHCpan trhough the sequence fasta file for each HLA

Value

a character

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