filterVariant: Variant filtering

In vivizhou/MDfilter: Mendelian disease variant filtering

Variant filtering

Description

This function filters the variants based on specified criteria and will print the filtering log on the console.

Usage

filterVariant(
  data.name,
  affected.id = NULL,
  unaffected.id = NULL,
  inheritance.pattern = NULL,
  femaleIDs = NULL,
  maleIDs = NULL,
  gene.name = NULL,
  frequency.col = NULL,
  freq.threshold = 1,
  protein.altering = FALSE,
  include.UTRs = FALSE,
  include.synonymous = FALSE,
  include.nonframeshift = TRUE,
  CADD.threshold = 0,
  save.path = NULL,
  save.txt = FALSE,
  label = "test",
  save.genelist = FALSE
)

Arguments

data.name	Data cleaned by ?clean.raw.data()
affected.id	IDs of the affected subjects,which should match the IDs in the data file (column name)
unaffected.id	IDs of the unaffected subjects,which should match the IDs in the data file (column name)
inheritance.pattern	Model of inheritance pattern. #"AR" = autosomal recessive/"AD"=autosomal dominant/"XLD"=X-linked dominant/"XLR"=X-linked recessive. You can specify "AD" for de novo variant filtering. If XLR is specified, female and male IDs should also be provided.
femaleIDs	Female and male IDs should also be provided.
maleIDs	Female and male IDs should also be provided.
gene.name	Specify the gene list to run candidate gene analysis.Example:gene.name = c("ALPL", "COL1A1", "PLS3")
frequency.col	Specify the column names of the frequencies to be used for filtering. For example: frequency.col = c("ExAC_All", "X1000G_ALL", "ExAC_NFE", "X1000G_EUR")
freq.threshold	The threshold of the frequency used for filtering.
protein.altering	Only include protein altering variants.
include.UTRs	On top of protein altering variants, TRUE=also include UTRs
include.synonymous	On top of protein altering variants, TRUE=also to include synonymous variants
include.nonframeshift	TRUE=also to include nonframeshift variants
CADD.threshold	The threshold of the CADD score used for filtering
save.path	Specify save path. If not specified the data will be saved at the working directory.
save.txt	TRUE=Save the returned data frame into a txt file.
label	Specify the label of the saved file.
save.genelist	TRUE=Save the filtered gene list into a txt file.

Value

A data frame of cleaned annotated data.

vivizhou/MDfilter documentation built on May 21, 2022, 2:15 a.m.