averageMGC: Compute the average mappability and GC scores over a set of...

In chandlerzuo/mbasic: Matrix Based Analysis for State-space Inference and Clustering.

Description

Compute the average mappability and GC scores over a set of genomic intervals.

Usage

averageMGC(target, m.prefix, m.suffix = NULL, gc.prefix, gc.suffix = NULL)

Arguments

target	A RangedData object for the target intervals.
m.prefix	A string for the prefix of the mappability files.
m.suffix	A string for the suffix of the mappability files. See details for more information. Default: NULL.
gc.prefix	A string for the prefix of the GC files.
gc.suffix	A string for the suffix of the GC files. See details for more information. Default: NULL.

Details

If m.suffix is NULL, then a single file with name m.prefix should include mappability scores of all chromosomes, and this file is read. Alternatively, all mappability files with m.prefix<chrXX>m.suffix are read. The gc.suffix argument has similar effects.
target has to be a RangedData object. If it is not sorted, then the elements are reordered. Users have to make sure that other data sources must follow the same ordering in the elements.

Value

A RangedData object with two extra fields from the input argument target:

mappability	The average mappability scores for the sorted elements of target.
GC	The average GC scores for the sorted elements of target.

Author(s)

Chandler Zuo [e-mail]

chandlerzuo/mbasic documentation built on May 13, 2019, 3:24 p.m.