SNP_QC: Do quality control of SNP data downloaded from TCGAbiolinks

In huerqiang/GeoTcgaData: Processing Various Types of Data on GEO and TCGA

Do quality control of SNP data downloaded from TCGAbiolinks

Description

Do quality control of SNP data downloaded from TCGAbiolinks

Usage

SNP_QC(
  snpData,
  geon = 0.02,
  mind = 0.02,
  maf = 0.05,
  hwe = 1e-06,
  miss = "NoCall"
)

Arguments

snpData	data.frame of SNP data downloaded from TCGAbiolinks
geon	filters out all variants with missing call rates exceeding the provided value (default 0.02) to be removed
mind	filters out all samples with missing call rates exceeding the provided value (default 0.02) to be removed
maf	filters out all variants with minor allele frequency below the provided threshold
hwe	filters out all variants which have Hardy-Weinberg equilibrium exact test p-value below the provided threshold
miss	character of miss value

Value

data.frame

Examples

# use demo data
snpDf <- matrix(sample(c("AA", "Aa", "aa"), 100, replace = TRUE), 10, 10)
snpDf <- as.data.frame(snpDf)
sampleGroup <- sample(c("A", "B"), 10, replace = TRUE)
result <- SNP_QC(snpDf)

huerqiang/GeoTcgaData documentation built on March 21, 2024, 1:42 a.m.