filter_dds_features: Filter lowly expressed features from a DESeq2DataSet...
In bryancquach/omixjutsu: Utilities for omics analysis tasks

filter_dds_features

R Documentation

Filter lowly expressed features from a DESeq2DataSet (deprecated)

Description

Removes expression features below a given threshold from a DESeq2DataSet object.

Usage

filter_dds_features(
  dds,
  count_cutoff,
  min_sample_fraction = NULL,
  threshold_variable = NULL,
  use_min_fraction = T,
  approximate = F
)

Arguments

`dds`	The DDS object from which to filter features.
`count_cutoff`	The minimum number of counts required for a feature for greater than `min_sample_fraction` proportion of samples to retain the feature.
`min_sample_fraction`	The minimum proportion of samples with greater than `count_cutoff` counts to retain a feature.
`threshold_variable`	Name of the binary variable to use for calculating sample fractions.
`use_min_fraction`	If `TRUE`, uses the smaller of the sample fractions calculated from the `threshold_variable`. Otherwise uses the larger of the sample fractions.
`approximate`	If `TRUE`, round `min_sample_fraction` to a whole number ending in '0' or '5'.

Details

Included for backwards compatibility only. Use low_expression_filter instead. Filters out features considered lowly expressed from a DDS object using a count threshold and sample proportion set by the user. The sample proportion can also be estimated by calculating proportions of values from a binary variable specified by the user.