getNormFactor {SAGElyzer}R Documentation

Functions that get normalization factors for SAGE libraries

Description

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.

Usage

getNormFactor(normalize = c("min", "max", "none"), libs)
queryInfoDB(libCol = "libname",
                        infoCol = c("filename", "minfactor", "maxfactor"))

Arguments

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

Details

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.

Value

Both getNormFactor and queryInfoDB return a data frame containing normalization factors for a set of SAGE libraries.

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

http://www.ncbi.nlm.nih.gov/SAGE/

See Also

SAGELyzer

Examples

# No example is given as database support is required

[Package SAGElyzer version 1.4.2 Index]