getYeastData {AnnBuilder}R Documentation

Functions to get/process yeast genome data

Description

These functions extract data from the yeast genome web site based on a set of arguments.

Usage

getYeastData(url, extenName, cols2Keep, sep)
readBadData(url, sep)
findNumCol(fewLines, sep)

Arguments

url url a character string for the url where yeast data are stored
extenName extenName a character string for the name of the data file of interest. The name can be a file name or with subdirectory names under "url"
cols2Keep cols2Keep a vector of index for the columns to be extracted from the data file
sep sep a character string for the separater used to separate data columns in the data file
fewLines fewLines a set of character strings separated by a new line that is going to be used to determine how many data columns each line has

Details

The yeast genome web site has files stored in or in subdirectories of ftp://genome-ftp.stanford.edu/pub/yeast/data_download/ that can be downloaded. getYeastData extracts data from a given file. The functions are used by an object of YG-class to extract data.

Some of the data in the web site may not be well fomatted (e.g. with missing columns). readBadData deals with these type of data files.

findNumCol figures out how many data columns a file contains based on a few entries from that file.

Value

getYeastData returns a matrix containing data.
readBadData returns a matrix.
findNumCol returns an integer.

Note

The functions are part of the Bioconductor project at Dana-Farber Cancer Institute to provide Bioinformatics functionalities through R

Author(s)

Jianhua Zhang

References

ftp://genome-ftp.stanford.edu/pub/yeast/data_download/

See Also

YG-class

Examples

# Url may change but was correct at the time of coding
url <- "ftp://genome-ftp.stanford.edu/pub/yeast/data_download/"
temp <- getYeastData(url, "chromosomal_feature/SGD_features.tab",
                         cols2Keep = c(6, 1), sep = "\t")

[Package AnnBuilder version 1.4.21 Index]