keep_variable-methods: Keep top variable features across elements

In nanny: High-Level Data Analysis and Manipulation in 'tidyverse' Style

Description

keep_variable() takes as imput a 'tbl' formatted as | <element> | <feature> | <value> | <...> | and returns a 'tbl' with the filtered most variable features. The formula used is from limma::plotMDS (Robinson et al., 2010, <doi:10.1093/bioinformatics/btp616>)

Usage

keep_variable(.data, .element, .feature, .value, top = Inf, transform = NULL)

## S4 method for signature 'spec_tbl_df'
keep_variable(.data, .element, .feature, .value, top = Inf, transform = NULL)

## S4 method for signature 'tbl_df'
keep_variable(.data, .element, .feature, .value, top = Inf, transform = NULL)

Arguments

.data	A 'tbl'
.element	A character name of the element column
.feature	A character name of the transcript/gene column
.value	A character name of the read count column
top	An integer. How many top genes to select
transform	A function to use to tranforma the data internalli (e.g., log1p)

Details

\lifecycle

maturing

...

Value

A 'tbl' with filtered features

A 'tbl' with filled abundance

A 'tbl' with filled abundance

Examples

keep_variable(mtcars_tidy, car_model, feature, value, top=10)

nanny documentation built on July 1, 2020, 10:20 p.m.