getYeastData {AnnBuilder} | R Documentation |
These functions extract data from the yeast genome web site based on a set of arguments.
getYeastData(url, extenName, cols2Keep, sep) readBadData(url, sep) findNumCol(fewLines, sep)
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 |
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.
getYeastData
returns a matrix containing data.
readBadData
returns a matrix.
findNumCol
returns an integer.
Jianhua Zhang
ftp://genome-ftp.stanford.edu/pub/yeast/data_download/
## Not run: # 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") ## End(Not run)