Test if the gene expression is associated with pseudotime values (binning)

Test if the gene expression is associated with pseudotime values (binning)

Usage

temporalTest_bin(
  expr,
  pseudotime,
  pseudotime_permute = NULL,
  knot = 0,
  maxknotallowed = 10,
  numbin = 10
)

Arguments

expr

The normalized gene expression matrix. Rows represent genes and columns represent cells

pseudotime

The vector of user-provided pseudotime values

pseudotime_permute

A list of permuted pseudotime values from subsampled cells. Each element in the list has the same format of the argument pseudotime

knot

Number of knots (0 by default) or "auto" for automatic selection

maxknotallowed

A user-defined maximum number of knots (10 by default)

numbin

Number of bins (10 by default)

Value

A data frame with the p-value (FDR) and test statistic for each gene (each row)