searchPMC: Search PMC text and tables

In cstubben/pmcXML: Tools to parse full text XML documents from PMC Open Access

Description

Search PMC text and tables for a specific pattern

Usage

searchPMC(x, pattern, caption = TRUE, before = FALSE, after = FALSE, ignore.case = TRUE, ...)

Arguments

x	output from pmcText or pmcTable or pmcSupp
pattern	character string containing a regular expression
caption	include caption in collapsed table rows
before	include sentence before match
after	include sentence after match
ignore.case	ignore case
...	other options passed to grep

Details

Searches text and collpased tables using grep and returns a data.frame with section title and sentence (or table name and row).

Value

A data.frame

Author(s)

Chris Stubben

See Also

pmcText

Examples

## Not run: 
doc <- pmcOAI("PMC2231364" )
txt <- pmcText(doc)
searchPMC(txt, "virulen")
searchPMC(txt, "pathway")
searchPMC(txt, "accession")
# regular expression
searchPMC(txt, "[ACTGN]{6}")   # seqeunce
searchPMC(txt, "YPO[0-9]{4}")  # locus tag
searchPMC(txt, "[A-Z][a-z]{2}[A-Z]", ignore.case=FALSE)  # protein name

## End(Not run)

cstubben/pmcXML documentation built on May 14, 2019, 12:25 p.m.