get_test_data: Test data

In robinweide/GENOVA: GENOVA: expore the Hi-C

Test data

Description

Retrieves a test contacts object from a local cache at either 40k or 150k resolution. The test data only contains human chromosomes 21 and 22.

Usage

get_test_data(res, download = FALSE)

Arguments

res	The resolution of test data to use. Either "40k" or "150k".
download	A logical(1). If FALSE (default), will not download the data if it cannot be found in the cache. If TRUE, data is downloaded when not found in the cache.

Details

The data originates from wildtype Hap1 cells from the Haarhuis et al. (2017) publication. The full data is available in raw fastq files or valid pair files at GEO accession GSE95014. The data were mapped against the 'hg19' reference genome using HiC-Pro v2.7.7.

The test data only needs to be downloaded only once as it is stored in a local cache. The local cache can be cleared using the erase_GENOVA_cache() function.

Value

A GENOVA contacts at 40k or 150k resolution.

Examples

## Not run: 
# Fails the first time
exp <- get_test_data("40k")

# Should succees if `download = TRUE`
exp <- get_test_data("40k", download = TRUE)

# From now on, it should succeed
exp <- get_test_data("40k")

# Additional calls with `download = TRUE` do not re-download the data.
exp <- get_test_data("40k", download = TRUE)

## End(Not run)

robinweide/GENOVA documentation built on March 14, 2024, 11:16 p.m.