Equivalent to `strawr::straw` for `.cool` and `.mcool` files

Reads the cooler file, finds the appropriate matrix and slice of data, and outputs as data.frame in sparse upper triangular format. Currently only supporting "observed" matrixes.

Usage

coolStraw(norm, fname, chr1loc, chr2loc, binsize)

Arguments

norm

Normalization to apply. Must be one of the normalizations in the given file. Use `readCoolNormTypes(fname)` for accepted normalization types

fname

path to .cool or .mcool file

chr1loc

first chromosome location, in the format "chr1:start1:end1"

chr2loc

second chromosome location, in the format "chr2:start2:end2"

binsize

The bin size in basepairs. Must be one of the resolutions in the given file. Use `readCoolBpResolutions(fname)` for accepted binsizes

Value

data.frame of a sparse matrix of data from cool file. x,y,counts

Details

Normalizations are applied following the convention of the format they come from. `"BALANCE"` reads cooler's own `weight` column, which holds multiplicative biases, so counts are multiplied by the weight of each bin. Any other normalization is read from a like-named bin column and divided out instead, matching the divisive convention of juicer vectors carried into cooler files by converters such as hic2cool, and therefore matching `strawr::straw()`.