RFpairs_to_Iset: Convert restriction fragment annotation and restriction...

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

Description

Convert restriction fragment annotation and restriction fragment pair objects to an InteractionSet object.

Usage

RFpairs_to_Iset(RFanno, RFpairs, binned = FALSE)

Arguments

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.
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.
binned	Boolean, whether the matrix is already binned. Defaults to FALSE.

Value

An InteractionSet object.

Examples

# Iset <- RFpairs_to_Iset(RFanno, RFpairs)

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