romicsFilterVariable: romicsFilterVariable()

In PNNL-Comp-Mass-Spec/RomicsProcessor: omics-oriented package for reproducible and sharable data processing pipelines

romicsFilterVariable()

Description

Filters Romics_objects based on their variable names or statistics note that ALL the filters will be taken in consideration simultaneously

Usage

romicsFilterVariable(
  romics_object,
  ANOVA_filter = "p",
  p = 0.05,
  variable_names = "none",
  statCol = "none",
  statCol_filter = "<=0.05",
  statCol2 = "none",
  statCol2_filter = "<=0.05",
  mode = "keep"
)

Arguments

ANOVA_filter	Either 'none', 'p' or 'padj'. Indicates if an the ANOVA filter has to be used to plot the Heatmap (only the features below the filter will be displayed on the heatmap)
p	Numerical of length 1 indicating the value of the ANOVA_filter cutoff (anything below this value will be conserved).
variable_names	A character vector that enable to filter based on the names of the variables, if variable_name set to 'none' the filter won't be applied.
statCol	A column contained in the statistical layer of the romics_object, the list of columns can be obtained by using the function romicsCalculatedStats().
statCol_filter	Character to indicate how this column should be filtered (e.g. '<=0.05','>0.05','==1', '==TRUE', '>2')
statCol2	A column contained in the statistical layer of the romics_object, the list of columns can be obtained by using the function romicsCalculatedStats().
statCol2_filter	Character to indicate how this column should be filtered (e.g. '<=0.05','>0.05','==1', '==TRUE', '>2')
mode	Either 'keep' or 'drop' to indicate if the variable should be kept or droped based on the filters.

Author(s)

Geremy Clair

PNNL-Comp-Mass-Spec/RomicsProcessor documentation built on March 18, 2023, 5:14 a.m.