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

In seasoncloud/Alleloscope: Allele-specific copy number genotyping for single cell sequencing data

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.

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

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.
snp_ind	A numeric vector indexing the SNPs to be included.
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 March 17, 2023, 1:14 a.m.