combine.replicates: combine.replicates
In chicane: Capture Hi-C Analysis Engine

Description Usage Arguments Details Value References Examples

Merge biological replicates.

1	combine.replicates(replicates, method = c("sum", "weighted-sum"))

`replicates`	list of data table objects from `prepare.data`
`method`	string specifying the method for merging replicates. Options are 'sum' and 'weighted-sum'.

The parameter method determines which method is used for merging replicates. Available options are weighted-sum and sum.

'weighted-sum' implements the size factor scaling approach used in DEseq, rounded to the closest integer. See Anders and Huber 2010 for details.

'sum' is the naive sum of counts across biological replicates.

Data table object containing merged data, where counts are stored in colums

`count.i`	count of interaction in ith replicate
`count`	count after merging replicates

Anders, Simon, and Wolfgang Huber. "Differential expression analysis for sequence count data." Genome biology 11.10 (2010): R106.

if( bedtools.installed() ) {
	  # preprocess data
	  bam <- system.file('extdata', 'Bre80_2q35.bam', package = 'chicane');
	  baits <- system.file('extdata', '2q35.bed', package = 'chicane');
	  fragments <- system.file('extdata', 'GRCh38_HindIII_chr2.bed.gz', package = 'chicane');
	  input.data <- prepare.data(
	  bam = bam, 
	  baits = baits, 
	  fragments = fragments
	  );

	  # combined two datasets into one
  merged <- combine.replicates(list(input.data, input.data));
 }