find.indels.location.by.location: find the place (exon) of the indel sequence in annotation and...

In tangshao2016/neoantigenR: neoantigen prediction from NGS sequencing data

Description

find the place (exon) of the indel sequence in annotation and predicted genes

Usage

find.indels.location.by.location(chosen.gene, chose.pacbio.transcript.id,
  indel.seq, pacbio.protein.sequences, gene.df.pacbio,
  reference.gff.info.chosen, pacbio.isof.ids,
  compute.query.exon.details = FALSE, compute.database.exon.details = FALSE)

Arguments

chosen.gene	the gene of interest
chose.pacbio.transcript.id	chosen gene's prediction name
indel.seq	the chosen gene's alternative sequences
pacbio.protein.sequences	the protein sequence of the predicted gene
gene.df.pacbio	the data frame of the predicted genes (Gff)
reference.gff.info.chosen	the data frame of the annnotated genes
pacbio.isof.ids	the predicted gene's prediction id
compute.query.exon.details	whether to find the neoantigen's position in predictions
compute.database.exon.details	whether to find the neoantigen's position in annotations

Value

a vector of the predicted gene's genomic locations and locations in annotations

tangshao2016/neoantigenR documentation built on May 21, 2019, 3:04 a.m.