summarizeBam: Summarise descriptive Bam stats

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

Summarise descriptive Bam stats

Description

Summarise descriptive Bam stats

Usage

summarizeBam(
  bamfile = NULL,
  total_count = TRUE,
  total_mapped_count = TRUE,
  chrM_count = TRUE,
  duplicate_count = TRUE,
  coverage_by_mapped = TRUE,
  genome_length_bp = 3.2e+09,
  gc_metrics = FALSE,
  loci_coverage_metrics = FALSE,
  customized_count = FALSE,
  customized_count_mapqFilter = NA_integer_,
  customized_count_isPaired = NA,
  customized_count_isProperPair = NA,
  customized_count_isUnmappedQuery = NA,
  customized_count_hasUnmappedMate = NA,
  customized_count_isMinusStrand = NA,
  customized_count_isMateMinusStrand = NA,
  customized_count_isFirstMateRead = NA,
  customized_count_isSecondMateRead = NA,
  customized_count_isSecondaryAlignment = NA,
  customized_count_isNotPassingQualityControls = NA,
  customized_count_isDuplicate = NA,
  customized_count_isSupplementaryAlignment = NA,
  ...
)

Arguments

bamfile	Bam file
total_count	Boolean. default = TRUE, which means calculating the total number of reads.
total_mapped_count	Boolean. Default = TRUE, which mean calculating the number of mapped reads, and these reads must have mate reads.
chrM_count
duplicate_count
coverage_by_mapped
genome_length_bp
customized_count
customized_count_mapqFilter
customized_count_isPaired
customized_count_isProperPair
customized_count_isUnmappedQuery
customized_count_hasUnmappedMate
customized_count_isMinusStrand
customized_count_isMateMinusStrand
customized_count_isFirstMateRead
customized_count_isSecondMateRead
customized_count_isSecondaryAlignment
customized_count_isNotPassingQualityControls
customized_count_isDuplicate
customized_count_isSupplementaryAlignment
...

Value

tibble object (i.e. a dataframe)

Author(s)

Haichao Wang

Examples

## Not run: 

 summarizeBam(bamfile = "/path/to/bamfile.bam")

## End(Not run)

hw538/cfDNAPro documentation built on Nov. 28, 2024, 12:13 p.m.