getNormFactor {SAGElyzer}R Documentation

Functions that get normalization factors for SAGE libraries


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


See Also



# No example is given as database support is required

[Package SAGElyzer version 1.4.2 Index]