read_bam_insert_metrics: Calculate insert sizes from a curated GRanges object

In hw538/cfDNAPro: cfDNAPro extracts and Visualises biological features from whole genome sequencing data of cell-free DNA

Calculate insert sizes from a curated GRanges object

Description

Calculate insert sizes from a curated GRanges object

Usage

read_bam_insert_metrics(
  bamfile = NULL,
  fragment_obj = NULL,
  chromosome_to_keep = paste0("chr", 1:22),
  strand_mode = 1,
  genome_label = "hg19",
  outdir = FALSE,
  isize_min = 1L,
  isize_max = 1000L,
  ...
)

Arguments

bamfile	The bam file name.
chromosome_to_keep	Should be a character vector containing the seqnames to be kept in the GRanges object. Default is paste0("chr", 1:22).
strand_mode	Usually the strand_mode = 1 means the First read is aligned to positive strand. Details please see GenomicAlignments docs.
genome_label	The Genome you used in the alignment. Should be "hg19" or "hg38" or "hg38-NCBI. Default is "hg19". Note: "hg19" will load BSgenome.Hsapiens.UCSC.hg19 package, which is Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg19, based on GRCh37.p13) and stored in Biostrings objects; "hg38" will load BSgenome.Hsapiens.UCSC.hg38 package, which is Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, based on GRCh38.p13) and stored in Biostrings objects. "hg38-NCBI" will load BSgenome.Hsapiens.NCBI.GRCh38 package, which is full genome sequences for Homo sapiens (Human) as provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.
outdir	The path for saving rds file. Default is FALSE, i.e. not saving.
isize_min	min fragment length to keep, default is 1L.
isize_max	max fragment length to keep, default is 1000L.
...	Further arguments passed to or from other methods.

Value

This function returns a dataframe with two columns: "insert_size" and "All_Reads.fr_count".

Author(s)

Haichao Wang

Examples

## Not run: 

object <- read_bam_insert_metrics(bamfile = "/path/to/bamfile.bam")

## End(Not run)

hw538/cfDNAPro documentation built on Aug. 13, 2024, 2:58 p.m.