Man pages for ICBI/neoantigeR
neoantigen prediction from NGS sequencing data
| att.info | the attribute information of the gff file |
| chosen.column.indicies | the chosen column of gff file (to remove unused columns from... |
| compute.database.exon.details | look for the genomic location of the indel sequence in the... |
| compute.query.exon.details | look for the genomic location of the indel sequence in the... |
| coverage.file | coverage file to calculate sequence coverage for indel... |
| dataDir | the directly where data is stored |
| find.indels.location.by.location | find the place (exon) of the indel sequence in annotation and... |
| gene.df.pacbio | the data frame of predicted gene models |
| gff.file | the gff file in the dat frame mode |
| gff.names | the gff file's gene names |
| gffRead | read the gff gene prediction files |
| is.installed | check if a package is installed or not |
| mainDir | the directly where code and example data are stored |
| max.mismatch.size | at most 1000 amino is different from the annotation |
| minimum.flanking.region.size | mimimum anchor size in the indel region |
| minimum.sequence.similarity | the alternative isoform and reference protein sequence must... |
| min.mismatch.size | at least 3 amino acids must be different from the annotation |
| neoantigenR.get.Model | retrieve the predicted gene's exon coordinates and prepare... |
| neoantigenR.get.peptides | compute neoantigens using the novel algorithm after the... |
| neoantigenR.initialize | initialize the parameters and functions for neoantigen... |
| neoantigenR.write | write the predicted neoantigens for final results |
| org | the organism used to search protein database |
| output.folder | the folder of the output files |
| pacbio.gencode.overlapping.file | the predicted gff file intersecting with reference gene... |
| pacbio.gff | the predicted gff file |
| pacbio.isof.ids | the isoform or gene names from predicted gff model |
| percOverlap | the alternative isoform and reference protein sequence must... |
| protein.database.file.name | the path for reference protein database file (Swiss-uniprot) |
| reference.gff | the annotated gene in data frame mode |
| reference.gff.file | the path for reference annotated gene database file |
| reference.gff.info | the annotated gene in data frame mode with attributes... |
| reference.gff.info.chosen | the annotated gene models for chosen genes |
| refseq.pacbio.name.ids | the predicted gene model's gene ids (prediction names) |
| retrieve.geneName.pacbioID.mapping.v2 | read the gff gene prediction data frame |
| sample.pacbio.gencode.id.mapping | the mapping between predicted gene names and reference... |
| target.gene.list | the gene list finally chosen for neoantigen analysis |
| uniprot.human.database | the uniprot human dataset in data frame |
| uniprot.protein.names.new | the human protein names from uniprot |
| uniprot.protein.swissprot.index | the human protein names from uniprot swissport (only the rows... |
| use.reference.annotation.gff | indicate whether we will use reference gene annotation or now |
| validate.in.database.boolean | whether to validate indels in the annotated protein database |
| write.dna.seq.by.reference.genome | indicate whether we will write dna sequence for protein... |
| write.dna.sequence.reference | write the dna sequence of a predicted gene based on reference... |
