Test if the gene expression is associated with spatial locations (binning)

Test if the gene expression is associated with spatial locations (binning)

Usage

spatialTest_bin(expr, coord, knot = 0, maxknotallowed = 5, numbin = 10)

Arguments

expr

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

coord

The matrix of spatial locations. Rows represent spots/cells. The column named "row" ("col") represents row (column) coordinates

knot

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

maxknotallowed

A user-defined maximum number of knots (5 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)