exportResults: Export Results

Description

Export the results from a chicagoData object to disk, or to a GenomicInteractions object.

Usage

exportResults(cd, outfileprefix, scoreCol = "score", cutoff = 5, b2bcutoff = NULL, format = c("seqMonk", "interBed", "washU_text"), order = c("position", "score")[1], removeMT=TRUE)
exportToGI(cd, scoreCol="score", cutoff=5, b2bcutoff=NULL, order=c("position", "score")[1], removeMT=TRUE)

Arguments

A chicagoData object.

outfileprefix

A character string that forms the prefix for each output file.

scoreCol

The column of intData(cd) that contains the score.

cutoff

The score cutoff.

b2bcutoff

If desired, an alternative score cutoff for bait-to-bait interactions.

format

The file format(s) to output. If a multiple formats are supplied as a vector, then all of these formats will be outputted.

Supported formats are: "seqMonk", "interBed", "washU_text" and, for advanced users, "washU_track".

order

Should output be ordered by position or score?

removeMT

Logical. If TRUE, remove any interactions involving mitochondrial DNA from the output.

Value

exportResults(): NULL.exportToGI(): a GenomicInteractions object. Anchor one is the bait, anchor two is the other end.

Details

Important notes on the washU formats: Most users will prefer "washU_text" output to "washU_track" output. The "washU_text" output can be uploaded to the washU browser directly. To do this, open the browser, select "Add custom tracks", and use the "Got text files instead? Upload them from your computer" link near the bottom of the page.

The "washU_track" output needs to be hosted elsewhere. You can then link the browser to the data via the "Interaction - pairwise interaction" button on the "Add custom tracks" page.

If you get the warning "WashU Browser track format could not be finalized due to absence of bgzip or tabix", this could be because you have not installed SAMtools and htslib. You can check with system2("tabix") and system2("bgzip"). Sometimes RStudio has issues with reading $PATH - you can check this with system2("echo", "$PATH"). Consider running the command in R, outside of RStudio, to fix this problem.

If all else fails, and you need "washU_track" output, then you can manually perform the final steps yourself by running: bgzip _washU_track.txt and tabix -p bed .txt.gz.

Examples

Run this code

data(cdUnitTest)

##modifications to cdUnitTest, ensuring it uses correct design directory
designDir <- file.path(system.file("extdata", package="Chicago"), "unitTestDesign")
cdUnitTest <- modifySettings(cd=cdUnitTest, designDir=designDir)

##create a temporary directory, export output there
tempDirectory <- tempdir()
print(tempDirectory)
exportResults(cdUnitTest, outfileprefix = file.path(tempDirectory, "unitTestOutput"))

GI <- exportToGI(cdUnitTest)