anchor_pmids: check columns of a dataframe for numerical tokens of 7 or 8...

Description Usage Arguments Value Note Examples

View source: R/setup_lambert.R

Description

check columns of a dataframe for numerical tokens of 7 or 8 digits and create HTML anchors to pubmed.gov constituting a link to a PMID

Usage

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anchor_pmids(dataframe)

Arguments

dataframe

a data.frame instance

Value

data.frame with HTML anchors to pubmed.gov inserted where 7- or 8-digit numbers are found

Note

The method of isolating putative PMIDs is peculiar to patterns found in the comment fields of annotated TF table (supplemental table S1 found in https://www.cell.com/cms/10.1016/j.cell.2018.01.029/attachment/88c0eca1-66f9-4068-b02e-bd3d55144f79/mmc2.xlsx of PMID 29425488). When DT::datatable is called on the output of this function with escape=FALSE the PMIDs will render as hyperlinks. Note that column 1 is assumed to be an ENSEMBL ID which could have 7 or 8 digits but is handled differently

Examples

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litdf = data.frame(id="ENSG00000116819", a="Binds the same GCCTGAGGC sequence as the other AP-2s (PMID: 24789576)",
     stringsAsFactors=FALSE)
anchor_pmids(litdf)

TFutils documentation built on May 2, 2020, 2:01 a.m.