OmitPoorVariants: A function to remove rows with a high ratio of missing data...

In laurentlab-mpipz/rsurvival: Process genotype data from survival experiment

Description

A function to remove rows with a high ratio of missing data from a dataframe. (e.g. variants from genotype)

Usage

OmitPoorVariants(gt, min.qual, dp = NULL, verbose = TRUE)

Arguments

gt	A dataframe to process (e.g. a genotype dataframe)
min.qual	The minimum present data ratio under which the row will be deleted from the dataframe (from 0 to 1)
dp	An optionnal dataframe on which the process of gt will be executed too (e.g. a depth dataframe)
verbose	Logical. If TRUE (default), report status of the process along the execution.

Value

A dataframe or a list of dataframes. If the parameter dp is not set, return the gt dataframe without its rows where the missing data ratio was too high. If the dp is set, return the modified gt as list$gt; list$dp is the modified dp dataframe with the same missing rows as list$gt.

See Also

OmitPoorSamples

Examples

## Not run: 
OmitPoorVariants(genotype, 0.15)
OmitPoorVariants(genotype, 0.2, dp = depth)
OmitPoorVariants(genotype, 0.2, verbose = FALSE)

## End(Not run)

laurentlab-mpipz/rsurvival documentation built on May 29, 2019, 9:14 a.m.