# Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

## Documentation for package ‘signatureSearch’ version 1.16.0

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

## Help Pages

signatureSearch-package | Environment for Gene Expression Signature Searching Combined with Functional Enrichment Analysis
addGESSannot | Add Compound Annotation Info to GESS Result Table
addMOA | Add MOA annotation to drug data frame
add_pcid | Add PCID to drug data frame
append2H5 | Append Matrix to HDF5 File
build_custom_db | build_custom_db
calcGseaStatBatchCpp | Calculates GSEA statistic valus for all gene sets in 'selectedStats' list.
cellNtestPlot | Number of Tests in Cell Types
cell_info | LINCS 2017 Cell Type Information
cell_info2 | LINCS 2020 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 | FEA Methods
dsea_hyperG | FEA Methods
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
enrichReactome | Reactome Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enriched Reactome pathways with FDR control from hypergeometric test.
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
gessResult | Constructor for 'gessResult-class'
gessResult-class | gessResult object
gess_cmap | GESS Methods
gess_cor | GESS Methods
gess_fisher | GESS Methods
gess_gcmap | GESS Methods
gess_lincs | GESS Methods
gess_res_vis | GESS Result Visualization
getALLEG | getALLEG
getDb | getDb
getDEGSig | Draw GESs from Reference Database
getSig | Draw GESs from Reference Database
getSPsubSig | Draw GESs from Reference Database
getTreats | Get Treatment Information
get_targets | Target Gene/Protein IDs for Query Drugs
gmt2h5 | Convert GMT to HDF5 File
gseGO2 | Modified GSEA with GO Terms
gseKEGG2 | Modified GSEA with KEGG
gseReactome | Modified GSEA with Reactome
head | Return the First Part of an Object
head-method | Return the First Part of an Object
lincs_expr_inst_info | Instance Information of LINCS Expression Database
lincs_pert_info | LINCS 2017 Perturbation Information
lincs_pert_info2 | LINCS 2020 Perturbation Information
lincs_sig_info | LINCS Signature Information
list2df | Named list to data frame
list_rev | Reverse list
mabsGO | MeanAbs Enrichment Analysis for GO
mabsKEGG | MeanAbs Enrichment Analysis for KEGG
mabsReactome | MeanAbs Enrichment Analysis for Reactome
matrix2h5 | Write Matrix to HDF5 file
meanExpr2h5 | Calculate Mean Expression Values of LINCS Level 3 Data
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
read_gmt | Read in gene set information from .gmt files
result | Method to Extract Result Slots
result-method | Method to Extract Result Slots
runWF | Run the Entire GESS/FEA Workflow
set_readable | Set Readable
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
tarReduce | Show Reduced Targets
tsea_dup_hyperG | FEA Methods
tsea_mabs | FEA Methods
tsea_mGSEA | FEA Methods
vec_char_redu | Reduce Number of Character