quality_assessment: Quality assessment of whole genome Hi-C data.

In AnnikaGable/chromium: Analyze and visualize high throughput chromatin interaction data, such as Hi-C or ChIA-PET

Description

Calculate number of ligation products (treated as interactions), number of inter- and intrachromosomal interactions, and distances between interactions.

Usage

quality_assessment(RFpairs, RFanno, Iset = NULL)

Arguments

RFpairs	A dataframe with two columns containing restriction fragment pairs. The restriction fragment with the lower ID is always in the left column, and all restriction fragments are sorted in ascending order first by the left column and then by the right colunn.
RFanno	A dataframe giving the genomic annotation of the restriction fragments. Columns are: chromosome, start of restriction fragment, end of restriction fragment, restriction fragment ID. The table is sorted by chromosomal position and restriction fragments are numbered along their genomic position.
Iset	An InteractionSet object with lossFunction from normalization in its metadata.

Details

here go the details

Value

A list with the quality assessment values interactionCount, interchromosomal, intrachromosomal, contactDistances, and if it exist, the lossFunction values of each iteration of the normalization.

AnnikaGable/chromium documentation built on May 5, 2019, 6:04 a.m.