Gene Set Networking Analysis Package

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Documentation for package ‘GSNA’ version 0.1.4.1

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Bai_CiHep_DN.cerno Bai et al. Data Sets.
Bai_CiHep_dorothea_DN.Gsea Bai et al. Data Sets.
Bai_CiHep_dorothea_UP.Gsea Bai et al. Data Sets.
Bai_CiHep_v_Fib2.de Bai et al. Data Sets.
Bai_CiKrt_DN.cerno Bai et al. Data Sets.
Bai_CiKrt_v_Fib2.de Bai et al. Data Sets.
Bai_data Bai et al. Data Sets.
Bai_empty_expr_mat Bai et al. Data Sets.
Bai_gsc.tmod Bai et al. Data Sets.
buildGeneSetNetworkGeneric buildGeneSetNetworkGeneric
buildGeneSetNetworkJaccard buildGeneSetNetworkJaccard
buildGeneSetNetworkLF buildGeneSetNetworkLF, buildGeneSetNetworkLFFast-deprecated
buildGeneSetNetworkLFFast buildGeneSetNetworkLF, buildGeneSetNetworkLFFast-deprecated
buildGeneSetNetworkOC buildGeneSetNetworkOC
buildGeneSetNetworkSTLF buildGeneSetNetworkSTLF
color2IntV color2IntV
combineRGBMatrices combineRGBMatrices
complement complement
contrasting_color contrasting_color
distMat2Rank distMat2Rank
distMat2UnitNormRank distMat2UnitNormRank negDistMat2UnitNormRank
extract_david_GSC extract_david_GSC
gsc2tmod gsc2tmod
gsIntersect gsIntersect
gsIntersectCounts gsIntersectCounts
gsnAddPathwayData gsnAddPathwaysData
gsnAddPathwaysData gsnAddPathwaysData
gsnAssignSubnets gsnAssignSubnets
GSNData GSNData
gsnDendroSubnetColors gsnDendroSubnetColors, gsnDendroSubnetColors_dark
gsnDendroSubnetColors_dark gsnDendroSubnetColors, gsnDendroSubnetColors_dark
gsnDistanceHistogram gsnDistanceHistogram
gsnFilterGeneSetCollectionList gsnFilterGeneSetCollectionList
gsnHierarchicalDendrogram gsnHierarchicalDendrogram
gsnImportCERNO gsnImportCERNO
gsnImportDAVID gsnImportDAVID
gsnImportGenericPathways gsnImportGenericPathways
gsnImportGSEA gsnImportGSEA
gsnImportGSNORA gsnImportGSNORA
gsnMergePathways gsnMergePathways
gsnORAtest gsnORAtest
gsnORAtest_cpp gsnORAtest_cpp
gsnParedVsRawDistancePlot gsnParedVsRawDistancePlot
gsnPareNetGenericHierarchic gsnPareNetGenericHierarchic
gsnPareNetGenericToNearestNNeighbors gsnPareNetGenericToNearestNNeighbors
gsnPlotNetwork gsnPlotNetwork
gsnSubnetSummary gsnSubnetSummary
gsnSubset gsnSubset
gsnToIgraph gsnToIgraph
gsn_default_distance gsn_default_distance, gsn_distances, pw_id_col, pw_stat_col, pw_sig_order, pw_stat_col_2, pw_sig_order_2, pw_n_col, pw_type
gsn_default_distance<- gsn_default_distance, gsn_distances, pw_id_col, pw_stat_col, pw_sig_order, pw_stat_col_2, pw_sig_order_2, pw_n_col, pw_type
gsn_distances gsn_default_distance, gsn_distances, pw_id_col, pw_stat_col, pw_sig_order, pw_stat_col_2, pw_sig_order_2, pw_n_col, pw_type
intV2Color intV2Color
lfisher_cpp lfisher_cpp
lse lse
makeFilteredGenePresenceAbsenceMatrix makeFilteredGenePresenceAbsenceMatrix
makeLinearNColorGradientFunction makeLinearNColorGradientFunction
makeOneColorEncodeFunction makeOneColorEncodeFunction
makeSymmetricDist makeSymmetricDist
makeTwoColorEncodeFunction makeTwoColorEncodeFunction
negative negative
negDistMat2UnitNormRank distMat2UnitNormRank negDistMat2UnitNormRank
nzLog10 nzLog10
nzLog10.old nzLog10.old
pick_MappedGeneSymbol pick_MappedGeneSymbol
plot.GSNData plot plot.GSNData
print.GSNData print.GSNData
pw_id_col gsn_default_distance, gsn_distances, pw_id_col, pw_stat_col, pw_sig_order, pw_stat_col_2, pw_sig_order_2, pw_n_col, pw_type
pw_id_col<- gsn_default_distance, gsn_distances, pw_id_col, pw_stat_col, pw_sig_order, pw_stat_col_2, pw_sig_order_2, pw_n_col, pw_type
pw_n_col gsn_default_distance, gsn_distances, pw_id_col, pw_stat_col, pw_sig_order, pw_stat_col_2, pw_sig_order_2, pw_n_col, pw_type
pw_n_col<- gsn_default_distance, gsn_distances, pw_id_col, pw_stat_col, pw_sig_order, pw_stat_col_2, pw_sig_order_2, pw_n_col, pw_type
pw_sig_order gsn_default_distance, gsn_distances, pw_id_col, pw_stat_col, pw_sig_order, pw_stat_col_2, pw_sig_order_2, pw_n_col, pw_type
pw_sig_order<- gsn_default_distance, gsn_distances, pw_id_col, pw_stat_col, pw_sig_order, pw_stat_col_2, pw_sig_order_2, pw_n_col, pw_type
pw_sig_order_2 gsn_default_distance, gsn_distances, pw_id_col, pw_stat_col, pw_sig_order, pw_stat_col_2, pw_sig_order_2, pw_n_col, pw_type
pw_sig_order_2<- gsn_default_distance, gsn_distances, pw_id_col, pw_stat_col, pw_sig_order, pw_stat_col_2, pw_sig_order_2, pw_n_col, pw_type
pw_stat_col gsn_default_distance, gsn_distances, pw_id_col, pw_stat_col, pw_sig_order, pw_stat_col_2, pw_sig_order_2, pw_n_col, pw_type
pw_stat_col<- gsn_default_distance, gsn_distances, pw_id_col, pw_stat_col, pw_sig_order, pw_stat_col_2, pw_sig_order_2, pw_n_col, pw_type
pw_stat_col_2 gsn_default_distance, gsn_distances, pw_id_col, pw_stat_col, pw_sig_order, pw_stat_col_2, pw_sig_order_2, pw_n_col, pw_type
pw_stat_col_2<- gsn_default_distance, gsn_distances, pw_id_col, pw_stat_col, pw_sig_order, pw_stat_col_2, pw_sig_order_2, pw_n_col, pw_type
pw_type gsn_default_distance, gsn_distances, pw_id_col, pw_stat_col, pw_sig_order, pw_stat_col_2, pw_sig_order_2, pw_n_col, pw_type
pw_type<- gsn_default_distance, gsn_distances, pw_id_col, pw_stat_col, pw_sig_order, pw_stat_col_2, pw_sig_order_2, pw_n_col, pw_type
read_david_data_file read_david_data_file
read_gmt read_gmt
scoreJaccardMatrix_C scoreJaccardMatrix_C
scoreLFMatrix_C scoreLFMatrix_C
scoreOCMatrix_C scoreOCMatrix_C
tmod2gsc tmod2gsc
write_gmt write_gmt
yassifyPathways yassifyPathways