Patterning: Extract variants with user-specified variant pattern
In VPA: Variant Pattern Analyzer for next-generation sequencing study

Description Usage Arguments Details Value Author(s) See Also Examples

To prioritize variants in user-specified frequency pattern.

1	Patterning(x, pattern, paired=FALSE, not.covered=NULL, var.PL=NULL)

`x`	A `varlist` class data from the function `LoadFiltering`.
`pattern`	The variant frequency matrix. Each column of the matrix is defined as the minimum and maximum value of variant frequency for each group of interest.
`paired`	Logical value. Whether cases and controls are paired. If paired is TRUE, control group label in index file should be marked as control. Sample names should be matched between case and its matched control.
`not.covered`	Logical value for the position with sequence coverage less than specified depth. If TRUE, such low-coverage positions will be considered as variant. If FALSE, such low-coverage positions will be considered as reference. If it's NULL (default), such low-coverage positions will be filtered.
`var.PL`	A TRUE or FALSE vector for each group in the order of `pattern`. PL is used to label possible variant when `alter.PL` is not NULL in the function LoadFiltering. When filtering variants with specified frequency pattern, possible variants are considered as variants if TRUE. If FALSE, possible variants are considered as non-variants. If NULL, possible variants are considered as non-variants in all groups.

This function is used to extract variant with user-specified frequency pattern across study subjects. The pattern matrix is specified by users in advance. The column names should be matched with sample group names.

The value returned is a varlist, including VarVCF, VarFrequency, Pattern and Samples.

`VarVCF`	A list variants with user-specified frequency pattern in each sample.
`VarFrequency`	Variant frequencies for input positions.
`Sample`	Samples annotation from input file.

Qiang Hu

LoadFiltering

#setwd(system.file("extdata", package="VPA"))
#varflt <- LoadFiltering(file="index1.txt", filtering=TRUE, alter.PL=20,
#alter.AD=3)
#pattern <- cbind(A=c(1/4,1), B=c(0,0))
#varRes1 <- Patterning(varflt, pattern, var.PL=c(FALSE, TRUE))

VPA documentation built on May 2, 2019, 4:45 p.m.