Package index • jazzPanda

All functions

compute_permp(): Calculate a p-value for correlation with permutation.
create_genesets(): Convert the coordinates of set of genes into vectors.
.check_binning(): helper function to check the input of binning
.check_valid_input(): helper function to check the inputs passed to marker detection function
.check_valid_names(): helper function to check the names of gene/cluster/sample
.compute_observation(): Compute observation statistic for permutation framework
.compute_permutation(): Compute permutation statistics for permutation framework
.convert_data(): Convert SingleCellExperiment/SpatialExperiment/SpatialFeatureExperiment objects to list object for jazzPanda.
.create_cor_mg_result(): Create a marker gene result object for correlation approach
.create_lm_mg_result(): Create a marker gene result object for linear modelling approach
.get_cluster_vectors(): Create spatial vectors for clusters
.get_gene_vectors_cm(): Create spatial vectors for genes from count matrix and cell coordinates
.get_gene_vectors_tr(): Create spatial vectors for genes from transcript coordinates
.get_lasso_coef(): help function to get lasso coefficient for every cluster for a given model
get_cor(): Get observed correlation cor_mg_result
get_full_mg(): Get full lasso result from glm_mg_result
get_perm_adjp(): Get permutation adjusted p value from cor_mg_result
get_perm_p(): Get permutation p value from cor_mg_result
get_top_mg(): Get top lasso result from glm_mg_result
get_vectors(): Vectorise the spatial coordinates
jazzPanda-package jazzPanda: jazzPanda: A hybrid approach to find spatially relevant marker genes in image-based spatial transcriptomics data
lasso_markers(): Find marker genes with spatial coordinates
rep1_clusters: Rep1 selected cells
rep1_neg: Rep1 negative control genes within the selected region.
rep1_sub: A small section of Xenium human breast cancer rep1.
rep2_clusters: Rep2 selected cells
rep2_neg: Rep2 negative control genes within the selected region.
rep2_sub: A small section of Xenium human breast cancer rep2.