overlap: Combine chromosome conformation capture data with...

In mworkman13/HiCAGE: Hi-C Annotation and Graphics Ensemble

Description

Combine chromosome conformation capture data with segmentation and RNA data

Usage

overlap(hicfile, segmentfile, rnafile, bio_mart = "ensembl",
  martset = "hsapiens_gene_ensembl", webhost = "www.ensembl.org",
  hic.columns = c(1:6, 8), segment.columns = c(1:5), rna.columns = c(1,
  7), manual.priority = NULL, prune.priority = NULL)

Arguments

hicfile	The chromosome conformation capture datafile
segmentfile	The segmentation datafile from StateHub for example
rnafile	The RNA gene expression datafile containing Ensembl IDs and FPKM or TPM normalized expression values
bio_mart	BiomaRt used for pulling gene name and location data
martset	The specific mart or dataset used for genome information
webhost	Website host to connect to for downloading biomaRt data
hic.columns	Columns from the chromsome conformation capture data file that contain, in order, 'left chromosome', 'left start', 'left end', 'right chromosome', 'right start', 'right end', 'interaction score'
segment.columns	Columns from the segmentation data file that contain, in order, 'Chromosome', 'Start', 'End', 'Mark', 'Score'. Select only 'Chromosome', 'Start', 'End', and 'Mark' if manual prioritization is desired
rna.columns	Columns from the RNA-seq data file that contain, in order, 'GeneID', 'FPKM'
manual.priority	A concatenated list of state calls contained in the segmentation file that are to be used to manually prioritize state calls that fall within the same genomic region of the chromosome conformation capture file. This argument can be used if the segmentation file does not contain scores for state calls or if scores want to be overridden. The concatenated list should be in the form c("PAR", "EAR", "AR", "PPR", "EPR", "TRS", "HET") ordered from highest priority to lowest priority. In this case, only select columns containing'Chromosome', 'Start', 'End', and 'Mark' in the segmentation file using 'segment.columns'.
prune.priority	A concatenated list of state calls contained in the segmentation file that are to be used to prioritize state calls that both fall within the same genomic region of the chromosome conformation capture file and have identical scores. In this instance, segmentation scores will first be used to prioritize states, then prune.priority will be used to break ties. This argument is used so that only one interaction is defined for each line of the chromosome conformation capture file. Otherwise, multiple interactions can potentially be defined for a single chromsome interaction if two or more state calls in that region have identical segmentation scores. The concatenated list should be in the form c("PAR", "EAR", "AR", "PPR", "EPR", "TRS", "HET") ordered from highest priority to lowest priority. If manual.priority is set, this argument will have no effect

Value

Returns a GRanges with each chromsome conformation capture segment annotated with a prioritized segmentation mark, the nearest gene to the segmentation mark and the gene's FPKM expression data

Examples

hic_chr20 <- system.file("extdata", "hic_chr20.txt", package = "HiCAGE")
segment_chr20 <- system.file("extdata", "segment_chr20.bed",
    package = "HiCAGE")
rna_chr20 <- system.file("extdata", "rna_chr20.tsv", package = "HiCAGE")
example <- overlap(hicfile = hic_chr20,
                   segmentfile = segment_chr20,
                   rnafile = rna_chr20)

mworkman13/HiCAGE documentation built on May 23, 2019, 11:58 a.m.