Single Sample directioNAl Pathway Perturbation analYsis

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Documentation for package ‘sSNAPPY’ version 1.2.5

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

generate_permuted_scores	Permute sample labels to simulate null distribution of perturbation scores
generate_permuted_scores-method	Permute sample labels to simulate null distribution of perturbation scores
gsAnnotation_df	gsAnnotation_df: Categorization of KEGG pathways used for community annotation
logCPM_example	logCPM_example: Normalised logCPM of patient-derived explant models obtained from 5 ER-positive primamry breast cancer patients (GSE80098)
metadata_example	metadata_example: Sample metadata for malignant breast cancer tumours PDE from 5 ER+ breast cancer patients (GSE80098)
normalise_by_permu	Normalise test perturbation scores by permutation results
pathway_pert	Compute Single-sample Pathway-level Perturbation Score
plot_community	Visualise the community structure in significantly perturbed gene-set network
plot_gene_contribution	Plot genes' contribution to a specific pathway's perturbation as heatmap
plot_gs2gene	Plot pathways and genes contained in them as a network
plot_gs_network	Plot significantly perturbed gene-sets as a network
rank_gene_pert	Rank genes by perturbation scores within each sample
raw_gene_pert	Compute Gene-wise Perturbation Score
retrieve_topology	Retrieve pathway topology as weighted adjacent matrix
sSNAPPY	sSNAPPY: A package for testing directional single sample pathway perturbation
weight_ss_fc	Compute weighted single sample LogFCs from normalised logCPM
weight_ss_fc-method	Compute weighted single sample LogFCs from normalised logCPM