blank_filter {structToolbox}R Documentation

Blank filter

Description

Filters features based on the features present in blank samples. The median intensity of the samples is compared to the median intensity of the blank samples. Any sample not sufficiently more intense than the blank is removed. This is a wrapper for the blank filter in the PMP package.

Usage

blank_filter(
  fold_change = 20,
  blank_label = "blank",
  qc_label = "QC",
  factor_name,
  fraction_in_blank = 0,
  ...
)

Arguments

fold_change

numeric(1), fold_change minimum fold change between analytical and blank samples.

blank_label

character(1), class label used to identify blank samples.

qc_label

character(1) or NULL, class label used to identify QC samples.

factor_name

the column name of sample_meta to use

fraction_in_blank

numeric(1), value between 0 to 1 to specify fraction in how many blanks peaks should be present.

...

additional slots and values passed to struct_class

Value

A struct model object for applying a blank filter

Examples

D = iris_DatasetExperiment()
M = blank_filter(fold_change=2,
                 factor_name='Species',
                 blank_label='setosa',
                 qc_label='versicolor')
M = model_apply(M,D)

[Package structToolbox version 1.0.1 Index]