# Single Sample directioNAl Pathway Perturbation analYsis

## Documentation for package ‘sSNAPPY’ version 1.4.1

- 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 pathway's perturbation as a 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 adjacency 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