Identify genes of interest with SPARKX

A wrapper around the algorithm introduced by Zhu et al. 2021 to identify genes with spatial expression pattern with SPARK-X.

getSparkxGeneDf(object, threshold_pval = 1, arrange_pval = TRUE)

getSparkxGenes(object, threshold_pval)

getSparkxResults(object, test = TRUE)

runSparkx(object, numCores = 1, option = "mixture", verbose = NULL)

Arguments

object

An object of class spata2.

test

Character value. One of any. all, identical, not_identical and none. Specifies how input for tags is used to select image annotations. See section Selection of image annotation with tags for more information.

verbose

Logical. If set to TRUE informative messages regarding the computational progress will be printed.

(Warning messages will always be printed.)

Value

An updated spata object.

Author

Zhu, J., Sun, S. & Zhou, X. SPARK-X: non-parametric modeling enables scalable and robust detection of spatial expression patterns for large spatial transcriptomic studies. Genome Biol 22, 184 (2021). https://doi.org/10.1186/s13059-021-02404-0