split_baits: Regroups putative interactions by bait and calculates...

In cqgd/pky: Capture Hi-C calling algorithm

Description

Merges bin-wise data, calculates the p-values for putative interactions under the negative binomial model. Regroups putative interactions by bait rather than by distance bin.

Usage

split_baits(bins, residuals, log_file = NA)

Arguments

bins	List of data tables containing putative interactions that are binned by distance.
residuals	List containing residuals (adjusted read counts) for each bin (matching the interaction order).
log_file	Path to a log file.

Value

Data table with p-values, residuals and putative interaction attributes that can be sorted or split by bait ID.

Examples

base = system.file("extdata",package="peaky")
interactions_file = paste0(base,"/counts.tsv")
fragments_file = paste0(base,"/fragments.bed")
interactions = data.table::fread(interactions_file)
fragments = data.table::fread(fragments_file)

## Not run: 
BI = bin_interactions(interactions, fragments, bins=5)
models = by(BI$interactions, BI$interactions$dist.bin, model_bin, subsample_size=1000)
residuals = lapply(models, "[[", "residuals")
bins = split(BI$interactions, BI$interactions$dist.bin)

split_baits(bins, residuals)

## End(Not run)

cqgd/pky documentation built on Dec. 13, 2020, 3:32 a.m.