Fetch interactions from a File object
Usage
fetch(
file,
range1 = "",
range2 = "",
normalization = "NONE",
count_type = "int",
join = FALSE,
query_type = "UCSC",
type = "df"
)Arguments
- file
file from which interactions should be fetched.
- range1
first set of genomic coordinates of the region to be queried. Accepted formats are UCSC or BED format. When not provided, genome-wide interactions will be returned.
- range2
second set of genomic coordinates of the region to be queried. When not provided, range2 is assumed to be identical to range1.
- normalization
name of the normalization factors used to balance interactions. Specify "NONE" to return raw interactions.
- count_type
data type used to fetch interactions. Should be "int" or "float"
- join
join genomic coordinates onto pixels. When TRUE, interactions will be returned in bedgraph2 format. When FALSE, interactions will be returned in COO format. Ignored when type="dense".
- query_type
type of the queries provided through range1 and range2 parameters. Types of query supported: "UCSC", "BED".
- type
interactions format. Supported formats: "df", "dense".
Examples
if (FALSE) { # \dontrun{
f <- File("interactions.hic",
1000000)
fetch(f) # Fetch genome-wide interactions
fetch(f, "chr2L") # Fetch interactions overlapping a symmetric query
fetch(f,
"chr2L:0-10,000,000",
"chr3L:10,000,000-20,000,000") # Fetch interactions overlapping an asymmetric query
fetch(f, normalization="ICE") # Fetch ICE-normalized interactions
fetch(f, join=TRUE) # Fetch interactions together with their genomic coordinates
fetch(f,
"chr1\t0\t10000000",
query_type="BED") # Fetch interactions given a query in BED format
fetch(f, type="dense") # Fetch interactions in dense format (i.e. as a Matrix)
} # }