Man pages for ICBI/neoantigeR
neoantigen prediction from NGS sequencing data

att.infothe attribute information of the gff file
chosen.column.indiciesthe chosen column of gff file (to remove unused columns from...
compute.database.exon.detailslook for the genomic location of the indel sequence in the...
compute.query.exon.detailslook for the genomic location of the indel sequence in the...
coverage.filecoverage file to calculate sequence coverage for indel...
dataDirthe directly where data is stored
find.indels.location.by.locationfind the place (exon) of the indel sequence in annotation and...
gene.df.pacbiothe data frame of predicted gene models
gff.filethe gff file in the dat frame mode
gff.namesthe gff file's gene names
gffReadread the gff gene prediction files
is.installedcheck if a package is installed or not
mainDirthe directly where code and example data are stored
max.mismatch.sizeat most 1000 amino is different from the annotation
minimum.flanking.region.sizemimimum anchor size in the indel region
minimum.sequence.similaritythe alternative isoform and reference protein sequence must...
min.mismatch.sizeat least 3 amino acids must be different from the annotation
neoantigenR.get.Modelretrieve the predicted gene's exon coordinates and prepare...
neoantigenR.get.peptidescompute neoantigens using the novel algorithm after the...
neoantigenR.initializeinitialize the parameters and functions for neoantigen...
neoantigenR.writewrite the predicted neoantigens for final results
orgthe organism used to search protein database
output.folderthe folder of the output files
pacbio.gencode.overlapping.filethe predicted gff file intersecting with reference gene...
pacbio.gffthe predicted gff file
pacbio.isof.idsthe isoform or gene names from predicted gff model
percOverlapthe alternative isoform and reference protein sequence must...
protein.database.file.namethe path for reference protein database file (Swiss-uniprot)
reference.gffthe annotated gene in data frame mode
reference.gff.filethe path for reference annotated gene database file
reference.gff.infothe annotated gene in data frame mode with attributes...
reference.gff.info.chosenthe annotated gene models for chosen genes
refseq.pacbio.name.idsthe predicted gene model's gene ids (prediction names)
retrieve.geneName.pacbioID.mapping.v2read the gff gene prediction data frame
sample.pacbio.gencode.id.mappingthe mapping between predicted gene names and reference...
target.gene.listthe gene list finally chosen for neoantigen analysis
uniprot.human.databasethe uniprot human dataset in data frame
uniprot.protein.names.newthe human protein names from uniprot
uniprot.protein.swissprot.indexthe human protein names from uniprot swissport (only the rows...
use.reference.annotation.gffindicate whether we will use reference gene annotation or now
validate.in.database.booleanwhether to validate indels in the annotated protein database
write.dna.seq.by.reference.genomeindicate whether we will write dna sequence for protein...
write.dna.sequence.referencewrite the dna sequence of a predicted gene based on reference...
ICBI/neoantigeR documentation built on June 30, 2017, 12:01 a.m.