Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

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Documentation for package ‘signatureSearch’ version 1.18.0

• 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