summarizeBases-methods: summarizeBases

In sheng-liu/SeqData: A data structure and four simple tools build upon it for sequencing data analysis

Description

count base measurement (e.g methylation) on any genomic regions.

Usage

summarizeBases(obj=NULL,bamFile=character(0),annotationFile=character(0),baseReport=charcter(0),description=character(0))

Arguments

obj	A SeqData object.
bamFile	The full path to the sequencing data. The data needs to be in bam file format.
annotationFile	csv annotation file for specifying ranges of interest. It must includes the miminum five field: 'chrom','txSart','txEnd','strand' and 'name'.
baseReport	DNA methylaton report from methylaton aligners such as bismark, in the form of a csv file has minimu four columns "chromosome", "position", "strand", "count_methylated", "count_unmethylated". if strand information is not available, fill it with "*".
description	Optional. User can input short desciption for the output file, it will show up in the file name of the output file.

Details

the method can be applied to any parameters measured along genome. essentially, the function is to group the items in bases based on region provided, then comput whatever statistics over those groups. Internally, it calls getBaseAlignment.

Value

• baseTable.csv a csv file contains the base summarization.

Usage

summarizeBases(obj=NULL,bamFile=character(0),annotationFile=character(0),baseReport=charcter(0),description=character(0))

Examples

# summarizeBases(obj)
# summarizeBases(baseReport)
# summarizeBases(bamFile=bamFile,annotationFile=annotationFile)

sheng-liu/SeqData documentation built on May 29, 2019, 9:22 p.m.