filterGeneLists: Filter gene lists

In frankRuehle/systemsbio: Streamlined Analysis and Integration of Systems Biology Data

Description

Gene list are filtered for selected columns considering desired direction and/or transformation.

Usage

filterGeneLists(
  genes,
  newheader = NULL,
  filtercat1 = "adj.P.Val",
  filtercat1.decreasing = FALSE,
  filtercat1.function = abs,
  filtercat1.threshold = 0.05,
  filtercat2 = "logFC",
  filtercat2.decreasing = TRUE,
  filtercat2.function = abs,
  filtercat2.threshold = log2(1.5)
)

Arguments

genes	dataframe or character with path directing to table with genelist and columns to filter for.
newheader	NULL if genes already supplied with header. Character vector with new header otherwise.
filtercat1	column name of first category to filter genes (e.g. p-values). Skipped if NULL.
filtercat1.decreasing	(boolean): direction to order and filter filtercat1
filtercat1.function	select transforming function for filtercat1 (no quotes). e.g. abs for absolute values, identity for no transformation
filtercat1.threshold	Threshold for filtercat1 or 'top123' for (123) top Hits
filtercat2	column name of second category to filter genes (e.g. effect size). Skipped if NULL.
filtercat2.decreasing	(boolean): direction to order and filter filtercat2
filtercat2.function	select transforming function for filtercat2 (no quotes). E.g. abs for foldchanges.
filtercat2.threshold	Threshold for filtercat2 or 'top123' for top Hits

Details

The function filters a dataframe or a character directing to dataframe for up to two categories (e.g. p-value and foldchange). Columns for filter criteria must be included in the input dataframe genes. Values in filter criteria may be transformed e.g. to absolute values by filtercat.function = abs, which is needed for log foldchanges. No tranformation if filtercat.function = identity.

Value

dataframe filtered for desired criteria and sorted for filtercat1 (if not Null).

Author(s)

Frank Ruehle

frankRuehle/systemsbio documentation built on Sept. 14, 2020, 1:18 a.m.