match_reads_contigs: Sequence pattern matching of RNAseq reads and counts the...

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

Description

Sequence pattern matching of RNAseq reads and counts the number of breakpoint junction reads.

Usage

match_reads_contigs(Sample_ID, pdict_obj, RNAseqReads, contigSeqs = NULL)

Arguments

Sample_ID	character string of patient ID
pdict_obj	pdict class object form biostrings.
RNAseqReads	DNAstring set object with RNAseq reads to query
contigSeqs	DNAstring set object with fusion algorithm (eg STAR-fusion) derived fusion contig sequences

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"))

my_contigs <- data.frame(contig="AATGGCTATC", Name=paste0("seq",1)) %>% pull(contig,name=Name)
my_contigs <- Biostrings::DNAStringSet(my_contigs)

my_pdict_obj <- create_custom_pdict(theoretical_seqs_df=my_seqs)
my_bam_reads <- subset_bam("PAZZUM.03A.01R", breakpoint=list("16:1250000|16:1260000"), my_files_df)

evidence <- match_reads_contigs("PAZZUM.03A.01R", my_pdict_obj, my_bam_reads, contigSeqs=my_contigs)

## End(Not run)

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