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]