# Single Sample directioNAl Pathway Perturbation analYsis

## Documentation for package ‘sSNAPPY’ version 1.2.0

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

## Help Pages

compute_perturbation_score | Compute Single Sample Perturbation Score
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
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 tumors PDE from 5 ER+ breast cancer patients (GSE80098)
normalise_by_permu | Normalise test perturbation scores by permutation
plot_gs_network | Plot gene-set network
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