getDPStats {AnnBuilder}R Documentation

Functions to read in the statistics about a data package

Description

These functions generate a list showing the name, data of creation, number of genes for each rda file, and the actual number of genes that get mapped for each rda file.

Usage

getDPStats(baseF, pkgName, pkgPath, saveList = TRUE, isFile = TRUE)
getDate(pkgName, pkgPath, fromDesc)
getProbeNum(pkgName, pkgPath, noNA = FALSE)
matchProbes(baseF, pkgName, pkgPath, toMatch, isFile = TRUE)
getPBased()
formatABQCList(x)
countMapping(rdaName, noNA = FALSE)

Arguments

baseF baseF a character string for the name of a file that is going to be used as the base file to calculate the total number of probes and matched probes by a data package. Set to "" if there is no base file
pkgName pkgName a character string for the name of the data package of concern
pkgPath pkgPath a character string for name of the path to which the data package is stored.
noNA noNA a boolean to indicate whether counts will exclude entries with NA as the value.
saveList sageList a boolean indicating whether the results will be returned as a list only (FALSE) or saved to a file as well (TRUE)
toMatch toMatch a vector of character strings for the names of the rda files whose keys will be matched against the probe ids of a base file (baseF)
x x a list object produced by function getDPStats
fromDesc fromDesc a boolean that will get a date from a DESCRIPTION file if set TRUE or the current date if FALSE
isFile isFile a boolean that will be TRUE if baseF is the name of a file
rdaName rdaName a character string for the name of an rda file whose man page will be generated

Details

Date of creation is the date when the package was created using AnnBuilder and in most cases is not the date when the source file AnnBuilder used to create the rda files was created. The date when the source data were built are listed in the man page for the package (?package name).

The number of genes and number of genes mapped normally differ because not all genes in a given set can be mapped to annotation data. For probe based rda files (e. g. maps Affymetrix ids to annotation data), the number of mapped genes out of the total is given. For non-probe based rda files, only the total number of mapped items is given.

The total number of probes of each rda file will be checked against the total of the base file and the names of the rda files whose total is off will be listed.

Value

list A list with name and value pairs

Note

This function is part of the Bioconductor project at Dana-Farber Cancer Institute to provide Bioinformatics functionalities through R

Author(s)

Jianhua Zhang

See Also

ABPkgBuilder

Examples

# Run this code after changing the settings correctly
# Change the varaibles before you run the code
pkgName <- "hgu95a"
pkgPath <- "where/your/data/package/is"
# Call getABStats
# getDPStats(pkgName, pkgPath)

[Package AnnBuilder version 1.4.21 Index]