segmentJaccard: Jaccard-Index overlap test for classes of segments (genomic...

Description Usage Arguments Details

View source: R/segmenTools.R

Description

calculates the Jaccard index, including a simple permutation test, between different classes in a query and a target set of segments (genomic intervals), where coordinates have been converted to a continuous index over all chromosomes with coor2index. Note, that this ignores chromosome borders!

Usage

1
segmentJaccard(query, target, qclass, tclass, total, perm = 0, verb = 1)

Arguments

query

query set of segments

target

target set of segments

qclass

column name which holds a sub-classification (clustering) of the query segments, omit or pass empty string ("") to use all

tclass

column name which holds a sub-classification (clustering) of the target segments, omit or pass empty string ("") to use all

total

total length of the query range (genome length), if missing the start of the first segment is also used as end

perm

number of permutations to perform

verb

integer level of verbosity, 0: no messages, 1: show messages

Details

Reports the Jaccard index (J=intersect/union)) between two distinct sets of segments (genomic intervals). If argument perm>0, a simple permutation is performed, sampling randomly from all inter-segment distances and segment lengths, and ignoring optional query sub-classifications (argument qclass). Note, that chromosome ends are ignored. The total length of the query range (genome length, for both strands, if both are used) can be passed in argument total, and if missing the start of the first segment is also used as the distance of the final segment to the query range end. The results of the permutation test (argument perm>0) can be plotted directly with plotOverlaps.


raim/segmenTools documentation built on Nov. 9, 2018, 5:38 p.m.