examine_breakpoint_evidence: Workflow wrapper to extract RNAseq reads and search for...

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

Description

Workflow wrapper to extract RNAseq reads and search for custom breakpoint exon junction sequences.

Usage

examine_breakpoint_evidence(
  Sample_ID,
  fusion_data = NULL,
  breakpoint = NULL,
  file_manifest,
  Seqlens,
  fusion_theoretical_pdict,
  cicero.contig,
  TA.contigs
)

Arguments

Sample_ID	character string of patient ID
fusion_data	dataframe with fusion results from CICERO, TransAbyss, and STAR-Fusion concatenated
breakpoint	list class with breakpoint string
file_manifest	dataframe with Sample_ID and the full file path of the BAM file.
Seqlens	named numeric vector with chromosome lengths
fusion_theoretical_pdict	a pdict obj with computationally derived exon junction sequences
cicero.contig	a dataframe with contig sequences from CICERO output
TA.contigs	a dataframe with contig sequences from TransAbyss output

Examples

## Not run: 
my_seqs <- data.frame(Name=paste0("seq",1:10),Sequence=rep(c("ATCGCCCGTTA"), 10))
my_files_df <- data.frame(Sample="PAZZUM.03A.01R", filepath=dir("/path/to/sample.bam"))
chr_lengths <- c("16"=24000000)

my_pdict_obj <- create_custom_pdict(theoretical_seqs_df=my_seqs)

examine_breakpoint_evidence("PAZZUM.03A.01R", breakpoint=list("16:1250000|16:1260000"),
my_files_df,chr_lengths, my_pdict_obj, cicero_contig_df, transabyss_contig_df)

## End(Not run)

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