filter_misc: Filter data

In mrc-ide/mipmapper: Filtering and analysis of MIP panel genetic datasets

Description

Filter out miscellaneous unwanted values from data

Usage

filter_misc(dat, SNP_only = TRUE, group_Alt = TRUE, drop_irregular = TRUE)

Arguments

dat	MIP data. The data must have the following variables: Ref : Character for reference allele nucleotide Alt : Character for alternative allele nucelotide Coverage : The total read coverage as numerics Barcode_Count : The total barocdes recovered
SNP_only	Boolean detailing if subsetting should remove all cases where the ALT allele is longer than 1 nucleotide. Default = 'TRUE'
group_Alt	Boolean detailing whether all ALT alleles should be grouped together. Default = 'TRUE'
drop_irregular	Boolean detailing whether irregular data should be removed. This includes non integer barcode counts and any instances where there is less coverage than barcode counts. Default = 'TRUE'

Details

'filter_misc' takes a raw dataset and applies a series of filters that enable the removal of non-standarad ALT allele calls and long ALT calls. It also enables the filtering of irregular data, such as data with non integer counts of barcodes or more barcode counts than coverage.

Examples

dat <- dummy_data()
dat2 <- filter_misc(dat)
dim(dat2)[1] < dim(dat)[1]

mrc-ide/mipmapper documentation built on May 20, 2019, 3:27 p.m.