SnapATAC (version 1.0.0)

runNormJaccard: Normalize Jaccard Index Matrix

Description

This function takes a Snap obj as input with jmat slot and normalize for read depth effect.

Usage

runNormJaccard(obj, tmp.folder, method, row.center, row.scale, low.threshold,
  high.threshold, do.par, ncell.chunk, num.cores, seed.use)

Arguments

obj

A snap obj

tmp.folder

A non-empty character vector giving the directory name to save temp files.

method

A character class that indicates the normalization method to be used. This must be one of c("residual", "zscore").

row.center

A logical value indicating whether rows of the normalized jaccard inex matrix should be centered by subtracting the layer means (omitting 'NA's).

row.scale

A logical value indicating whether rows of the normalized jaccard index matrix should be scaled by dividing the (centered) layers of 'x' by their standard deviations if 'center' is 'TRUE'.

low.threshold

A numeric class that indicates the min value for normalized jaccard index [-5].

high.threshold

A numeric class that indicates the max value for normalized jaccard index [5].

do.par

A logical variable indicates if to run this in parallel using multiple processors [TRUE].

ncell.chunk

A numeric class that indicates number of cells to process per CPU node

num.cores

A numeric class that indicates the number of cores to use for calculation [1].

seed.use

A numeric class that indicates random seeding number [10].

Details

In theory, the entries in the jaccard index calculated by calJaccard() should reflects the true similarity between two cells, however, that is not the case. We observed that a cell of higher coverage tends to have a higher similarity with another cell regardless whether these two cells are similar or not. These biases, we termed as <U+201C>coverage bias<U+201D> also observed in other studies, can later result in misleading cell grouping. Therefore, it is cruicial to normalize the bias.

Examples

# NOT RUN {
data(demo.sp);
demo.sp = makeBinary(demo.sp);
demo.sp = runJaccard(obj=demo.sp, mat="bmat", do.par=FALSE, tmp.folder=tempdir());
demo.sp = runNormJaccard(obj=demo.sp, do.par=FALSE, tmp.folder=tempdir());

# }