Single Sample directioNAl Pathway Perturbation analYsis


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Documentation for package ‘sSNAPPY’ version 1.0.2

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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