Accessor for h5File path from an InteractionMatrix — path,InteractionMatrix-method • mariner

Returns the file path describing where the on-disk HDF5 data associated with the InteractionMatrix object is stored.

This method circumvents the `assays<-` and `path<-` methods for updating the HDF5 path because they are not accessible when the file path is broken.

Usage

# S4 method for InteractionMatrix
path(object)

# S4 method for InteractionMatrix
path(object) <- value

Arguments

object: InteractionMatrix object
value: String (length-one character vector) to use for path replacement.

Value

The path to the HDF5 file associated with the InteractionMatrix object.

Updates path to HDF5 file for the InteractionMatrix object.

Details

If the file no longer exists, the path is returned along with a warning.

This allows the file path to be updated even if the original linked data no longer exists.

Examples

## Load marinerData
if (!require("marinerData", quietly = TRUE))
    BiocManager::install("marinerData")

## Read .hic file paths
hicFiles <- c(
    marinerData::LEUK_HEK_PJA27_inter_30.hic(),
    marinerData::LEUK_HEK_PJA30_inter_30.hic()
)
#> see ?marinerData and browseVignettes('marinerData') for documentation
#> loading from cache
#> see ?marinerData and browseVignettes('marinerData') for documentation
#> loading from cache
names(hicFiles) <- c("FS", "WT")

#################################
## Accessing path to HDF5 data ##
#################################

## Create example interactions
x <- read.table(text="
        9 14000000 14500000 9 14500000 15000000
        9 89500000 90000000 9 89500000 90000000
        9 23500000 24000000 9 23500000 24000000")
x <- as_ginteractions(x)

## Extract 3 pixels from 2 hic files
imat <- pullHicPixels(x, hicFiles, 500e03)

## Access path
path(imat)
#> [1] "/tmp/RtmpwSTrvs/file17dd375bd601.h5"

#################################
## Updating path to HDF5 data ##
################################

## Create example interactions
x <- read.table(text="
        9 14000000 14500000 9 14500000 15000000
        9 89500000 90000000 9 89500000 90000000
        9 23500000 24000000 9 23500000 24000000")
x <- as_ginteractions(x)

## Extract 3 pixels from 2 hic files
h5File <- tempfile(fileext=".h5")
imat <- pullHicPixels(x, hicFiles, 500e03, h5File=h5File)

## Move file to new location
newFile <- tempfile(fileext="_new.h5")
file.rename(from=h5File, to=newFile)
#> [1] TRUE

## Update path
path(imat) <- newFile
path(imat)
#> [1] "/tmp/RtmpwSTrvs/file17dd77d4e83b_new.h5"