receptorAbundanceEstimation {STREAK}

Receptor abundance estimation for single cell RNA-sequencing (scRNA-seq) data using gene set scoring and thresholding.

Description

Performs receptor abundance estimation for m x n scRNA-seq target data using gene set scoring and thresholding. scRNA-seq target counts are normalized and reduced rank reconstructed (RRR) using the SPECK::randomizedRRR() function. Gene set scoring is next performed leveraging expression from the top most weighted genes based on the gene sets weights membership matrix with the VAM::vam() function. The resulting cell-specific gene set scores are then thresholded utilizing the Ckmeans.1d.dp::Ckmeans.1d.dp() function. Note that this function only performs normalization and does not perform any quality control (QC) checks on the inputted target scRNA-seq counts matrix. Any QC needed can be performed on the target matrix before passing it as an input to the function.

Usage

receptorAbundanceEstimation(
  target.rnaseq,
  receptor.geneset.matrix,
  num.genes = 10,
  rank.range.end = 100,
  min.consec.diff = 0.01,
  rep.consec.diff = 2,
  manual.rank = NULL,
  seed.rsvd = 1,
  max.num.clusters = 4,
  seed.ckmeans = 2
)

Arguments

target.rnaseq

m x n scRNA-seq counts matrix for m cells and n genes.

receptor.geneset.matrix

n x h Gene sets weights membership matrix.

num.genes

Number of top most weighted genes for subsequent gene set scoring and thresholding.

rank.range.end

See documentation for the randomizedRRR function from the SPECK package.

min.consec.diff

See documentation for the randomizedRRR function from the SPECK package.

rep.consec.diff

See documentation for the randomizedRRR function from the SPECK package.

manual.rank

See documentation for the randomizedRRR function from the SPECK package.

seed.rsvd

See documentation for the randomizedRRR function from the SPECK package.

max.num.clusters

See documentation for the ckmeansThreshold function from the SPECK package.

seed.ckmeans

See documentation for the ckmeansThreshold function from the SPECK package.

Value

• receptor.abundance.estimates - A m x h matrix consisting of abundance estimates for m cells in h receptors.

Examples

data("train.malt.rna.mat")
data("train.malt.adt.mat")
receptor.geneset.matrix.out <- receptorGeneSetConstruction(train.rnaseq =
                                         train.malt.rna.mat[1:100,1:80],
                                         train.citeseq =
                                         train.malt.adt.mat[1:100,1:2],
                                         rank.range.end = 70,
                                         min.consec.diff = 0.01,
                                         rep.consec.diff = 2,
                                         manual.rank = NULL,
                                         seed.rsvd = 1)
dim(receptor.geneset.matrix.out)
head(receptor.geneset.matrix.out)
data("target.malt.rna.mat")
receptor.abundance.estimates.out <- receptorAbundanceEstimation(target.rnaseq =
                                    target.malt.rna.mat[1:200,1:80],
                                    receptor.geneset.matrix =
                                    receptor.geneset.matrix.out,
                                    num.genes = 10, rank.range.end = 70,
                                    min.consec.diff = 0.01,
                                    rep.consec.diff = 2,
                                    manual.rank = NULL, seed.rsvd = 1,
                                    max.num.clusters = 4, seed.ckmeans = 2)
dim(receptor.abundance.estimates.out)
head(receptor.abundance.estimates.out)