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Bin MAF Data and Estimate MAF Metrics per Bin

Source: R/AIsegmentation.R
BinMaf.Rd

Bins input MAF data into fixed-size windows or fixed-snp-count window and calculates summary metrics (e.g., estimated MAF, nonzero counts) for each bin.

Usage

BinMaf(
  data,
  datatype,
  maxgap = 2e+06,
  snpnum = 20,
  maxbinsize = 1e+06,
  minbinsize = 5e+05,
  minsnpcov = 20
)

Arguments

data

A data frame or tibble containing at least Chromosome, Pos, Start, End and maf columns.

datatype

If individual tumor data then choose "tumor", if aggregated panel of normal samples choose "pon".

maxgap

Maximum gap size inside a bin. If exceed then start another bin.( default: 2000000)

snpnum

SNP number in each bin.( default: 20 )

maxbinsize

Maximum bin size.( default: 1000000 )

minbinsize

Minimum bin size.( default: 500000 )

minsnpcov

Minimum coverage of SNP sites to be included. ( default: 20 )

Value

A tibble with one row per bin and columns:

Chromosome

Chromosome identifier.

bin

Bin start coordinate.

Start

Minimum End value in the bin.

End

Maximum End value in the bin.

nonzero_count

Number of nonzero maf values in the bin.

each_maf

Semicolon-separated string of nonzero maf values in the bin.

gmm_mean, gmm_weight, gmm_G

Unnested maf or BAF metrics.