SPatial Analysis of Multiomics Measurements in R

Documentation for package ‘spammR’ version 0.99.26

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calc_centers	Calculate centers of spots/samples for distance based analysis
calc_diff_pairwiseSamples	Helper function for computing pairwise differences between sample values
calc_missingness	Calculate degree of missingness for each featurea and sample
calc_spatial_diff_ex	Identify differentially abundant features across image
convert_to_spe	Create a 'SpatialExperiment' object from data
distance_based_analysis	Identify multiomic features correlated with an distance to an image feature
enrich_gradient	Calculate functional or pathway enrichment from a gradient
enrich_ora	Calculate functional or pathway enrichment
impute_spe	Impute missing values based on spatial coordinates
oneKSoilsCoords	Soil sample coordinates for the sample information
oneKSoilsMeta	Soil samples from the 1000 soils project Row names indiciate KEGG Orthologs, Column names indicate locations Soil samples metadata for the sample information
pancMeta	Here is the data to be included in the spammR package
protMeta	Protein metadata for general uniprot data, including the pancProts column for the panc data
retrieve_metaspace_data	Retrieve data objects from metaspace
smallPancData	Pancreatic proteomics measurements from Gosline et al. proteomics study. Row names indicate individual proteins, columns indicate sample identifiers described in 'pancMeta'. Individual values show un-transformed abundance values for each protein. List of proteomic measurements in a list sorted from individual regions of the pancreas. A subset of the data at https://figshare.com/articles/dataset/spammR_Files/29250962
spatial_heatmap	Plot data in heatmap together with image
spatial_network	Plot network of correlated features
spat_reduce	Reduce a high resolution image measurement (origin) to a lower resolution measurement (target)
split_spe	Divide SPE object into smaller objects by column features
volcano_plot	Create a volcano plot from differential expression data