primoData: primoData

In pcaGoPromoter: pcaGoPromoter is used to analyze DNA micro array data

Description

primoData calculated the data objects used by primo().

Usage

primoData(promoters, matrices, cleanUpPromoters = TRUE)

Arguments

promoters	a list with promoter data. See details.
matrices	a list with matrices. See details.
cleanUpPromoters	Should some house-keeping procedures (remove dublets, map common name etc.) be preformed on promoters?

Details

primoData makes a custom data object for function primo().

primoData needs 2 arguments: promoters and matrices.

promoter must consist of 2 list: a list with the RefSeq names for all the promoters and a list with all the promoter sequences in lowercase letters. The length of the two lists must be the same.

The function pcaGoPromoters:::primoData.getPromoter( filename ) can be used to load promoter from a file in FASTA format.

matrices must consist of one list of lists. Each list element must have a unique name and holds 3 data elements: baseId, name and pwm. baseId is a character vector with a base id. name is a character vector with the common name for the matrix. pwm is a position weighted matrix with the base A,C,G,T in rows and the weights in columns.

Example of promoter and matrices data types is shown in the wiki at: ???

primoData returns an object of type primoData. It contains to list - threshold and promotersRefseqs.

thresholds is a list of lists. Each list element have a unique name and holds 4 data elements: baseId, name, pwmLength and maxScores. baseId is a charactor vector with a base id. name is a character vector with the common name for the matrix. pwmLength is the length of the position weighted matrix. maxScores holds the max score from all the promoters.

promotersRefseq is a list with the Refseq names for all the promoters. Some promoters can have one that one refseq name. These names maps to the maxScores from thresholds.

Value

primoData returns an object to be used by primo() as argument primoData.

Note

primoData takes very long time (many hours) to run. Install package 'multicore' and use a computer with multiple cores.

Author(s)

Morten Hansen [e-mail] and Jorgen Olsen [e-mail]

References

Stegmann, A., Hansen, M., et al. (2006). "Metabolome, transcriptome, and bioinformatic cis-element analyses point to HNF-4 as a central regulator of gene expression during enterocyte differentiation." Physiological Genomics 27(2): 141-155.

Examples

## Not run: 
myPrimoData <- primoData( myPromoters, myMatrices)

## End(Not run)

pcaGoPromoter documentation built on Oct. 31, 2019, 5:31 a.m.