genome_paint_format: Create JSON file for input into St. Jude Genome Paint

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

Description

Create JSON file for input into St. Jude Genome Paint

Usage

genome_paint_format(df, fusion_genes_GR)

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.
fusion_genes_GR	fusion_genes_GR is granges list object that contains genes that involved in the fusions in the input dataframe

Examples

## Not run: 
genesGR <- transcriptsBy(Grch37.txdb, by="gene")
fusion.df <- data.frame(Fusion.Category="CBFB-MYH11",
 FusionID="My Fusion Name",
 chromosomes_A="chr16",
 pos_A=00000100,
 chromosomes_B="chr16",
 pos_B=00000200)

formatted <- genome_paint_format(df=fusion.df, fusion_genes_GR = genesGR)


## End(Not run)

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