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Remove Variables with Low Expression

remove_low_expr.Rd

Filters variables based on median expression values. Variables with median expression values below certain percentile will be removed.

Usage

remove_low_expr(x, percentile = 0.05, by = NULL, strict = FALSE)

# S3 method for class 'glyexp_experiment'
remove_low_expr(x, percentile = 0.05, by = NULL, strict = FALSE)

# S3 method for class 'matrix'
remove_low_expr(x, percentile = 0.05, by = NULL, strict = FALSE)

# Default S3 method
remove_low_expr(x, percentile = 0.05, by = NULL, strict = FALSE)

Arguments

x

Either a glyexp_experiment object or a matrix.

percentile

The percentile for median expression values. Defaults to 0.05, i.e., the 5% lowest median expression values will be removed.

by

Either a column name in sample_info (string) or a vector specifying group assignments for each sample.

strict

If FALSE, remove a variable only if it passes the abundance thresholds in all groups. If TRUE, remove a variable if it passes the abundance thresholds in any group. Defaults to FALSE.

Value

For glyexp_experiment input, returns a modified glyexp_experiment object. For matrix input, returns a filtered matrix.