RunNetMHCIIPan: RunNetMHCIIPan

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

RunNetMHCIIPan(
  seqfile,
  alleles,
  rankS = 0.5,
  rankW = 10,
  rankF = 10,
  pepLength = 15
)

Arguments

seqfile	character with the file path of the fasta file (it should be .fasta and contain onle 1 sequence)
alleles	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

Details

run netMHCIIpan trhough the sequence fasta file for each MHCII Allele

Value

a character vector with Strong Binders (SB) and Weak Binders (WB)

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