fullCurate: fullCurate

In foster-gabe/PFExpTools: Tools for analysis of Plasmodium falciparum gene expression data

Description

Are you feeling really, spectacularly lazy? This is the function for you. If you know the GEO accession number of your expression set and the columns necessary for nameChange, this function will do the entire curation for you in one call.

Usage

fullCurate(
  GSE,
  platcols = c(1, 2),
  method = "blast",
  aliases = "current",
  transcripts = "current",
  match = 130,
  secmatch = 60,
  pct = 0.8,
  pullmeta = T
)

Arguments

GSE	This is the GSE accession number.
platcols	These are the columns necessary for the nameChange function; see nameChange for details.
method	These are the available methods for name changes; see nameChange for details.
aliases	IF method is 'aliases', list the alias file name or 'current' for a PlasmoDB download. See nameChange for details.
transcripts	If method is 'transcripts', this is the transcriptome fasta file, or if 'current' it will download the most recent file.
match	see curateExpData.
secmatch	See curateExpData.
pct	See curateExpData.
pullmeta	See curateExpData.

Value

See curateExpData.

foster-gabe/PFExpTools documentation built on May 25, 2020, 7:22 a.m.