filterGeneLists: Filter gene lists

Description Usage Arguments Details Value Author(s)

View source: R/HLP_filterGeneLists.R

Description

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

Usage

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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 July 3, 2018, 10:05 a.m.