# Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

## Documentation for package ‘signatureSearch’ version 1.0.0

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

## Help Pages

signatureSearch-package | Environment for Gene Expression Signature Searching Combined with Functional Enrichment Analysis
append2H5 | Append Matrix to HDF5 File
build_custom_db | build_custom_db
cell_info | Cell Type Information
chembl_moa_list | MOA to Gene Mappings
clue_moa_list | MOA to Drug Name Mappings
comp_fea_res | Plot for Comparing Ranking Results of FEA Methods
create_empty_h5 | Create Empty HDF5 File
dim | Dimensions of an Object
dim-method | Dimensions of an Object
drugs | Extract/Assign Drug Names for feaResult
drugs-method | Extract/Assign Drug Names for feaResult
drugs10 | Drug Names Used in Examples
drugs<- | Extract/Assign Drug Names for feaResult
drugs<--method | Extract/Assign Drug Names for feaResult
drug_cell_ranks | Summary ranking statistics across cell types
dsea_GSEA | Drug Set Enrichment Analysis (DSEA) with GSEA Algorithm
dsea_hyperG | Drug Set Enrichment Analysis (DSEA) with Hypergeometric Test
dtnetplot | Drug-Target Network Visualization
enrichGO2 | GO Term Enrichment with Hypergeometric Test
enrichKEGG2 | KEGG Pathway Enrichment with Hypergeometric Test
enrichMOA | MOA Category Enrichment with Hypergeometric Test
fea | Environment for Gene Expression Signature Searching Combined with Functional Enrichment Analysis
feaResult | Constructor for 'feaResult-class'
feaResult-class | feaResult object
GCT object | An S4 Class to Represent a GCT Object
gctx2h5 | Convert GCTX to HDF5 File
gess | Environment for Gene Expression Signature Searching Combined with Functional Enrichment Analysis
gessResult | Constructor for 'gessResult-class'
gessResult-class | gessResult object
gess_cmap | CMAP Search Method
gess_cor | Correlation-based Search Method
gess_fisher | Fisher Search Method
gess_gcmap | gCMAP Search Method
gess_lincs | LINCS Search Method
gess_res_vis | GESS Result Visualization
get_targets | Target Gene/Protein IDs for Query Drugs
gseGO2 | Modified GSEA with GO Terms
gseKEGG2 | Modified GSEA with KEGG
head | Return the First Part of an Object
head-method | Return the First Part of an Object
mabsGO | MeanAbs Enrichment Analysis for GO
mabsKEGG | MeanAbs Enrichment Analysis for KEGG
matrix2h5 | Write Matrix to HDF5 file
moa_conn | Summarize GESS Results on MOA Level
parse_gctx | Parse GCTX
qSig | Helper Function to Construct a 'qSig' Object
qSig-class | Class "qSig"
rand_query_ES | Generate WTCS Null Distribution with Random Queries
readHDF5chunk | Import HDF5 Data into SummarizedExperiment Object
result | Method to Extract Result Slots
result-method | Method to Extract Result Slots
show | show method
show-method | show method
signatureSearch | Environment for Gene Expression Signature Searching Combined with Functional Enrichment Analysis
sim_score_grp | Summary Scores by Groups of Cell Types
tail | Return the Last Part of an Object
tail-method | Return the Last Part of an Object
targetList | Target Sample Data Set
tsea_dup_hyperG | Target Set Enrichment Analysis (TSEA) with Hypergeometric Test
tsea_mabs | Target Set Enrichment Analysis (TSEA) with meanAbs
tsea_mGSEA | Target Set Enrichment Analysis (TSEA) with mGSEA Algorithm