Matrix_filter: Filter object based on cell number for each SNP, SNP number...

Description Usage Arguments Value

View source: R/Matrix_filter.R

Description

Filter object based on cell number for each SNP, SNP number for each cell, SNP variant allele frequency, and exclude the centromere and telomere regions.

Usage

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Matrix_filter(
  Obj = NULL,
  cell_filter = 5,
  SNP_filter = 10,
  min_vaf = 0,
  max_vaf = 1,
  centro = NULL,
  telo = NULL,
  snp_ind = NULL,
  plot_stat = TRUE,
  plot_vaf = TRUE
)

Arguments

Obj

An Alleloscope object.

cell_filter

An integer of minimum cell number for SNP selection.

SNP_filter

An integer of minimum SNP number for cell selection.

min_vaf

A numerical value in the range (0,1) of minimum SNP variant allele frequency in the pseudo bulk for SNP selection.

max_vaf

A numerical value in the range (0,1) of minimum SNP variant allele frequency in the pseudo bulk for SNP selection.

centro

A Matrix/ data.frame of centromere information.

telo

A Matrix/ data.frame of telomere information.

plot_stat

Logical (TRUE/FALSE). Whether or not to plot the summary statistics.

plot_vaf

Logical (TRUE/FALSE). Whether or not to plot the variant allele frequency for the pseudo bulk for all the chromosomes.

Value

A Alleloscope object after the filtering.


seasoncloud/Alleloscope documentation built on June 18, 2021, 7:24 p.m.