nanny (version 0.1.8)

keep_variable: Keep top variable features across elements

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

Value

A `tbl` with filtered features

A `tbl` with filled abundance

A `tbl` with filled abundance

Details

maturing

...

Examples

# NOT RUN {
keep_variable(mtcars_tidy, car_model, feature, value, top=10)


# }