StandardLR2: Ligand-Receptor scoring - mean of mean expressions

In JamesChoi94/SingleCellTools: Various Wrapper Functions + Tools For Single-Cell 'Omics

Description

Ligand-Receptor scoring - mean of mean expressions

Usage

StandardLR2(
  seurat.object,
  ref.path = NULL,
  lr.ref = NULL,
  split.by = NULL,
  min.pct = 0.1,
  assay = "RNA",
  slot = "data",
  resample = 1000,
  adjust.pval = FALSE,
  BPPARAM = bpparam()
)

Arguments

seurat.object	Seurat object containing RNA expression data.
ref.path	Character string of path to ligand-receptor pair reference list. LR pair reference must contain a column labeled "Pair.Name" with values for each LR pair. If NULL, lr.ref must be provided.
lr.ref	Data.frame of ligand-receptor pair reference. Must contain a column labeled "Pair.Name" with values for each LR pair. If NULL, ref.path must be provided.
split.by	Character string of a column name in slot(tmp,'meta.data') by which to split cells before calculating LR scores e.g. across multiple conditions or time-points.
min.pct	Numeric minimum percentage a ligand or receptor gene must be expressed in any cell cluster to be retained for LR scoring. Note: scores will still be calculated between pairs where one cluster expresses at 15% and the other at 0%. These scores should be filtered out at visualization (see: PlotLR).
assay	Character string to select which assay slot of Seurat object to use.
resample	Numeric number of times to sample cells for permutation test.
adjust.pval	Logical determining whether to perform max-T p-value adjustment.

Value

A data.frame containing results of the standard ligand-receptor analysis. The columns of the data.frame as as follow:

• 'Pair_name' : Name of ligand gene followed and separated by name of receptor gene.

• 'Score' : Average of mean ligand expression in ligand cluster and mean receptor expression in receptor cluster.

• 'pval' : Estimated p-value using a permutation test. See description for more method details.

• 'adj_pval' : Adjusted p-value using a max-T adjustment. See https://statistics.berkeley.edu/sites/default/files/tech-reports/633.pdf equation 11 for more details.

• 'Ligand_cell' : Ligand-expressing cell cluster.

• 'Receptor_cell' : Receptor-expressing cell cluster.

JamesChoi94/SingleCellTools documentation built on April 5, 2021, 9:27 p.m.