getNormFactor {SAGElyzer} | R Documentation |
SAGE libraries vary in the total number of tags so that counts need to be normalized across libraries. These functions get the normalization factors that are stored in a database table.
getNormFactor(normalize = c("min", "max", "none"), libs) queryInfoDB(libCol = "libname", infoCol = c("filename", "minfactor", "maxfactor"))
normalize |
normalize a character string for the means of
normalization. Have to be either "min", "max", or "none" |
libs |
libs a vector of character strings for the names of
SAGE libraries to be normalized |
libCol |
libCol a character string for the name of the
column in a database table where names of SAGE libraries are stored |
infoCol |
infoCol a vector of character strings for the
names of database columns where SAGE library information is kept |
The normalization factor is calculated by dividing the total number of tags for a given library by the maximum or minimum value across the library.
getNormFactor
returns the normalization factors for a
given set of SAGE libraries.
queryInfoDB
queries a database table containing
information about SAGE libries to get the normalization factor for
SAGE libraries.
Both getNormFactor
and queryInfoDB
return
a data frame containing normalization factors for a set of SAGE libraries.
The functions are part of the Bioconductor project at Dana-Farber Cancer Institute to provide Bioinformatics functionalities through R
Jianhua Zhang
http://www.ncbi.nlm.nih.gov/SAGE/
# No example is given as database support is required