define_exon_junctions: Provides Exon Number from Genomic Coordinates.

In jennylsmith/fusBreakpoint: Find fusion exon junction sequence reads from RNAseq BAM files

Description

Provides Exon Number from Genomic Coordinates.

Usage

define_exon_junctions(df, exon_ranges_GR, intron_ranges_GR = NULL)

Arguments

df	dataframe for a single fusion with the breakpoint of the fusion-genes divided into 4 columns, chromosome and position for each gene in the fusion.
exon_ranges_GR	GRanges list object that contains exon ranges of transcripts involved in the fusions in the input dataframe. No duplicated gene IDs - one transcript ID per one gene ID
intron_ranges_GR	GRanges list object that contains intron ranges of transcripts involved in the fusions in the input dataframe. No duplicated gene IDs - one transcript ID per one gene ID

Examples

## Not run: 
my_transcript_IDs <- c("ENSTXXX","ENSTXXXXX")
intronGR <- intronsByTranscript(Grch37.txdb, use.names=TRUE)[my_transcript_IDs]
update.intronGR <- mcol_intron_rank(intronGR)
exonGR <- exonsBy(Grch37.txdb, by="tx", use.names=TRUE)[my_transcript_IDs]
fusions.df <- data.frame(chromosome_A="chr16",pos_A=00000100, chromosome_B="chr16", pos_B=00000200)
junctions.df <- define_exon_junctions(fusions.df,exonGR,update.intronGR)

## End(Not run)

jennylsmith/fusBreakpoint documentation built on Oct. 7, 2021, 8:04 p.m.