nameChange: nameChange

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

Description

This function takes a platform or a file from GEO (a cut and paste from the full table view, really), and identifies the new genome assembly name for each probe using one of a few methods. This function is a wrapper for subfunctions that carry out each method. Now, there's little consistency to the way the files are organized on GEO- platform naming conventions are loose to non-existant, so you'll have to go have a look at the platform manually and make some decisions on what method will work best. This function will use the working directory as a storage unit for any files downloaded from PlasmoDB and any BLAST databases built for this process.

Usage

nameChange(
  platform,
  platcols = c(1, 2),
  method = "swap",
  aliases = NA,
  transcripts = NA,
  match = 130,
  secmatch = 60
)

Arguments

platform	This can be a platform accession number OR a filename for a platform. If a file, a simple cut/paste in to a txt file will work here (it's tab delimited by default).
platcols	This one is a bit complex so settle in. This must be a vector with a length of two. The first entry is the column name for the probe/feature name. This can be ID, GeneID, ProbeID, it's completely inconsistent among platforms and you need to manually determine this. The second entry depends on method. For "swap", it is the column representing GeneDB version 3 gene identifiers (if present). For the "alias" file, it must be the old GeneDB gene identifier. For the "blast" method, it must be the probe sequence.
method	There are 3 methods here; "swap" just takes the new gene name from the platform file (least accurate), "alias" will find new names based on the current PlasmoDB assembly file (not bad), "blast" will take a provided Annotated Transcripts file from PlasmoDB, blast each probe against it, and only keep probes that meet the bitscore criteria (default is 130 for perfect hit and 60 for minimal secondary hits- this is based on probe length, and you may want to research bit scores for the platform in question).
aliases	This is the filename of the "alias" file downloaded from PlasmoDB. Alternately, if you're feeling spectacularly lazy, you can set this to 'current' and the function will do all the heavy lifting for you.
transcripts	The fasta file containing the annotated transcripts; this can be obtained from PlasmoDB. Alternately, if you're feeling spectacularly lazy, you can set this to 'current' and the function will do all the heavy lifting for you.
match	The bitscore for a perfect primary match; only necessary if "blast" is selected, default is 130.
secmatch	The maxmium bitscore for secondary probe alignments; only necessary if "blast is selected, default is 60.

Value

This returns a data frame with two columns; first column is the original IDs, and second column is the corresponding new ID.

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