fixHeaderAndGo: Fix data.frame header for use with ReportingTools

In jmacdon/affycoretools: Functions useful for those doing repetitive analyses with Affymetrix GeneChips

Fix data.frame header for use with ReportingTools

Description

Internal function used to automatically test for columns that can be converted to links

Usage

fixHeaderAndGo(df, affy = TRUE, probecol = "PROBEID")

Arguments

df	A data.frame
affy	Boolean; does the data.frame contain Affymetrix probeset IDs?
probecol	Character. The column header containing Affymetrix probeset IDs. Defaults to "PROBEID".

Details

This is an internal function designed to test for the presence of Affymetrix Probeset IDs or Entrez Gene IDs, and if found, generate a list that can be passed to the ReportingTools publish function in order to generate hyperlinks. The underlying assumption is that the data will have been annotated using a Bioconductor annotation package, and thus Affy probeset IDs will have a column header "PROBEID", and Entrez Gene IDs will have a header "ENTREZID" (or any combination of upper and lowercase letters).

Value

Returns a list of length two (with names mdf and df). The mdf object can be passed to the publish using the .modifyDF argument, and the df object is input dat.frame with column names corrected to conform to affyLinks and entrezLinks, so links will be generated correctly.

Author(s)

Jim MacDonald

jmacdon/affycoretools documentation built on Feb. 25, 2023, 4:51 a.m.