Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

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Documentation for package ‘signatureSearch’ version 1.2.2

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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
calcGseaStatBatchCpp Calculates GSEA statistic valus for all gene sets in 'selectedStats' list.
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
getDEGSig Drawn Query GES from Reference Database
getSig Drawn Query GES from Reference Database
getSPsubSig Drawn Query GES from Reference Database
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
head Return the First Part of an Object
head-method Return the First Part of an Object
lincs_sig_info LINCS Signature Information
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
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
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 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
vec_char_redu Reduce Number of Character