hicdcdiff: hicdcdiff

In mervesa/HiCDCPlus: Hi-C Direct Caller Plus

hicdcdiff

Description

This function calculates differential interactions for a set of chromosomes across conditions and replicates. You need to install DESeq2 from Bioconductor to use this function.

Usage

hicdcdiff(
  input_paths,
  filter_file,
  output_path,
  bin_type = "Bins-uniform",
  binsize = 5000,
  granularity = 5000,
  chrs = NULL,
  Dmin = 0,
  Dmax = 2e+06,
  diagnostics = FALSE,
  DESeq.save = FALSE,
  fitType = "local"
)

Arguments

input_paths	a list with names as condition names and values as paths to gi_list RDS objects (see ?gi_list_validate for a detailed explanation of valid gi_list instances) saved with saveRDS or paths to .hic files for each replicate. e.g.,list( CTCF=c('~/Downloads/GM_CTCF_rep1_MAPQ30_10kb.rds', '~/Downloads/GM_CTCF_rep2_MAPQ30_10kb.rds'), SMC=c('~/Downloads/GM_SMC_rep1_MAPQ30_10kb.rds', '~/Downloads/GM_SMC_rep2_MAPQ30_10kb.rds'))
filter_file	path to the text file containing columns chr', startI, and startJ denoting the name of the chromosomes and starting coordinates of 2D interaction bins to be compared across conditions, respectively.
output_path	the path to the folder and name prefix you want to place DESeq-processed matrices (in a .txt file), plots (if diagnostics=TRUE) and DESeq2 objects (if DESeq.save=TRUE). Files will be generated for each chromosome.
bin_type	'Bins-uniform' if uniformly binned by binsize in bp, or 'Bins-RE-sites' if binned by number of restriction enzyme fragment cutsites!
binsize	binsize in bp if bin_type='Bins-uniform' (or number of RE fragments if bin_type='Bins-RE-sites'), e.g., default 5000
granularity	Desired distance granularity to base dispersion parameters on in bp. For uniformly binned analysis (i.e., bin_type=='Bins-uniform'), this defaults to the bin size. Otherwise, it is 5000.
chrs	select a subset of chromosomes' e.g., c('chr21','chr22'). Defaults to all chromosomes (except Y and M) in the filter_file.
Dmin	minimum distance (included) to check for significant interactions, defaults to 0. Put Dmin=1 to ignore D=0 bins in calculating normalization factors.
Dmax	maximum distance (included) to check for significant interactions, defaults to 2e6 or maximum in the data; whichever is minimum.
diagnostics	if TRUE, generates diagnostic plots of the normalization factors, geometric means of such factors by distance bin, as well as MA Plots (see DESeq documentation for details about MA plots). Defaults to FALSE.
DESeq.save	if TRUE, saves the DESeq objects for each chromosome as an .rds file in the output_path. Defaults to FALSE.
fitType	follows fitType in DESeq2::estimateDispersions. Allowable options are 'parametric' (parametric regression),'local' (local regression), and 'mean' (constant across interaction bins). Default is 'local'.

Value

paths of a list of three entities. outputpaths will have differential bins among those in filter_file. deseq2paths will have the DESeq2 object stored as an .rds file. Available if DESeq.save=TRUE plotpaths will have diagnostic plots (e.g., MA, dispersion, PCA) if diagnostics=TRUE.

Examples

outputdir<-paste0(tempdir(check=TRUE),'/')
hicdcdiff(input_paths=list(NSD2=c(
system.file("extdata", "GSE131651_NSD2_LOW_arima_example.hic",
package = "HiCDCPlus"),
system.file("extdata", "GSE131651_NSD2_HIGH_arima_example.hic",
package = "HiCDCPlus")),
TKO=c(system.file("extdata", "GSE131651_TKOCTCF_new_example.hic",
package = "HiCDCPlus"),
system.file("extdata", "GSE131651_NTKOCTCF_new_example.hic",
package = "HiCDCPlus"))),
filter_file=system.file("extdata", "GSE131651_analysis_indices.txt.gz",
package = "HiCDCPlus"),
         chrs='chr22',
         output_path=outputdir,
         fitType = 'mean',
         binsize=50000,
         diagnostics=FALSE)

mervesa/HiCDCPlus documentation built on June 8, 2022, 3:43 a.m.