keep_abundant,tidybulk-method {tidybulk}R Documentation

keep_abundant

Description

keep_abundant

Usage

## S4 method for signature 'tidybulk'
keep_abundant(
  .data,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  factor_of_interest = NULL,
  minimum_counts = 10,
  minimum_proportion = 0.7
)

Arguments

.data

A 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> |

.sample

The name of the sample column

.transcript

The name of the transcript/gene column

.abundance

The name of the transcript/gene abundance column

factor_of_interest

The name of the column of the factor of interest. This is used for defining sample groups for the filtering process.

minimum_counts

A real positive number. It is the threshold of count per million that is used to filter transcripts/genes out from the scaling procedure.

minimum_proportion

A real positive number between 0 and 1. It is the threshold of proportion of samples for each transcripts/genes that have to be characterised by a cmp bigger than the threshold to be included for scaling procedure.

Value

A 'tbl' with additional columns for the statistics from the hypothesis test (e.g., log fold change, p-value and false discovery rate).

[Package tidybulk version 0.99.23 Index]