Test if the gene expression is associated with spatial locations — spatialTest • PreTSA

Test if the gene expression is associated with spatial locations

Usage

spatialTest(expr, coord, knot = F, maxknotallowed = 5)

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: Whether to select the optimal number of knots automatically
maxknotallowed: A user-defined maximum number of knots (5 by default)

Value

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