bamrd: Reads the BAM file
In DobzhanskyCenterSPBU/rnaedt: Estimation of the RNA Editing Probability

Description Usage Arguments Value Author(s)

View source: R/bamrd.R

Separates data from the input BAM file into a number of data frames, each suitable for the further RNA editing analysis

bamrd(
  bam_file_name,
  reference_fasta,
  max_depth = 8000,
  min_base_quality = 13,
  min_mapq = 30,
  min_nucleotide_depth = 1,
  min_minor_allele_depth = 0,
  min_coverage = 0,
  use_noncanonical = TRUE,
  strand_specific = FALSE,
  single_end = TRUE
)

`bam_file_name`	A `character(1)` path to the input BAM file
`reference_fasta`	A `character(1)` path to the reference genome FASTA file
`max_depth`	An `integer(1)` maximum number of nucleotides to be included in pileup
`min_base_quality`	An `integer(1)` minimum QUAL value for each nucleotide in an alignment
`min_mapq`	An `integer(1)` minimum MAPQ value for an alignment to be included in pileup
`min_nucleotide_depth`	An `integer(1)` minimum count of each nucleotide at a given position required for said nucleotide to appear in the result
`min_minor_allele_depth`	An `integer(1)` left undocumented
`min_coverage`	An `integer(1)` minimum coverage for position to be included in final dataset
`use_noncanonical`	A `logical(1)` indicating whether to use (`TRUE`) all chromosomes from BAM including non-canonical ones'
`strand_specific`	A `logical(1)` indicating the presence either of the strand-specific (`TRUE`) RNA-seq experiment, or non-strand-specific (`FALSE`) one
`single_end`	A `logical(1)` indicating the presence of the single-end (`TRUE`) RNA-seq experiment

On strand_specific == TRUE the list of three data frames (with names pileup_table, messy_positions, and pairs), otherwise the list of only one data frame (with name pileup_table) suitable for the further RNA editing analysis

Irina Shchyukina

DobzhanskyCenterSPBU/rnaedt documentation built on July 26, 2020, 12:41 p.m.