Subset enriched pathways of RAV
subsetEnrichedPathways(
RAVmodel,
ind = NULL,
n = 10,
both = FALSE,
include_nes = FALSE
)PCAGenomicSignatures object. Also an output from
GSEA can be used.
A numeric vector containing the RAV number you want to check enriched pathways. If not specified, this function returns results from all the RAVs.
The number of top and bottom pathways to be selected based on normalized enrichment score (NES).
Default is FALSE, where only the top n pathways
will be printed. If it is set to TRUE, the output will contain both
top and bottom n pathways.
Defalt is FALSE. If it set to TRUE, the
output will include both description and NES of the enriched pathway.
A DataFrame with top and bottom n pathways from the
enrichment results.
data(miniRAVmodel)
# all RAVS in model
subsetEnrichedPathways(miniRAVmodel,n=5)
#> DataFrame with 5 rows and 20 columns
#> RAV1076.Description RAV338.Description RAV1467.Description
#> <character> <character> <character>
#> Up_1 REACTOME_METABOLISM_.. MIPS_PA700_20S_PA28_.. REACTOME_MITOTIC_PRO..
#> Up_2 REACTOME_HOST_INTERA.. REACTOME_RESPIRATORY.. REACTOME_CHROMOSOME_..
#> Up_3 MIPS_SPLICEOSOME REACTOME_RESPIRATORY.. REACTOME_3_UTR_MEDIA..
#> Up_4 KEGG_SPLICEOSOME MIPS_55S_RIBOSOME_MI.. REACTOME_INFLUENZA_L..
#> Up_5 REACTOME_ASSEMBLY_OF.. KEGG_PARKINSONS_DISE.. REACTOME_TRANSLATION
#> RAV1614.Description RAV294.Description RAV3071.Description
#> <character> <character> <character>
#> Up_1 REACTOME_DNA_REPLICA.. REACTOME_CELL_CYCLE_.. KEGG_PURINE_METABOLISM
#> Up_2 REACTOME_MITOTIC_M_M.. REACTOME_M_G1_TRANSI.. MIPS_55S_RIBOSOME_MI..
#> Up_3 REACTOME_CELL_CYCLE_.. REACTOME_MITOTIC_PRO.. PID_FOXM1PATHWAY
#> Up_4 REACTOME_CELL_CYCLE MIPS_55S_RIBOSOME_MI.. REACTOME_E2F_MEDIATE..
#> Up_5 REACTOME_CELL_CYCLE_.. REACTOME_MRNA_PROCES.. PID_ATR_PATHWAY
#> RAV1694.Description RAV438.Description RAV725.Description
#> <character> <character> <character>
#> Up_1 REACTOME_ADAPTIVE_IM.. REACTOME_METABOLISM_.. REACTOME_ADAPTIVE_IM..
#> Up_2 KEGG_PURINE_METABOLISM DMAP_ERY5 REACTOME_METABOLISM_..
#> Up_3 REACTOME_SIGNALING_B.. DMAP_ERY4 DMAP_ERY5
#> Up_4 REACTOME_DOWNSTREAM_.. REACTOME_POST_TRANSL.. DMAP_ERY4
#> Up_5 DMAP_ERY4 DMAP_ERY3 DMAP_ERY3
#> RAV1497.Description RAV501.Description RAV941.Description
#> <character> <character> <character>
#> Up_1 MIPS_28S_RIBOSOMAL_S.. REACTOME_TRANSCRIPTION IRIS_DendriticCell-C..
#> Up_2 MIPS_55S_RIBOSOME_MI.. REACTOME_METABOLISM_.. REACTOME_CHROMOSOME_..
#> Up_3 REACTOME_RESPIRATORY.. REACTOME_DNA_REPAIR PID_PLK1_PATHWAY
#> Up_4 KEGG_OXIDATIVE_PHOSP.. REACTOME_RESPIRATORY.. IRIS_CD4Tcell-Th1-re..
#> Up_5 REACTOME_RESPIRATORY.. REACTOME_CYCLIN_E_AS.. REACTOME_M_G1_TRANSI..
#> RAV2538.Description RAV1139.Description RAV884.Description
#> <character> <character> <character>
#> Up_1 REACTOME_CELL_CYCLE DMAP_ERY3 DMAP_ERY3
#> Up_2 REACTOME_CELL_CYCLE_.. KEGG_ALZHEIMERS_DISE.. REACTOME_METABOLISM_..
#> Up_3 REACTOME_DNA_REPLICA.. REACTOME_POST_TRANSL.. KEGG_ALZHEIMERS_DISE..
#> Up_4 REACTOME_MITOTIC_M_M.. REACTOME_APOPTOSIS KEGG_HUNTINGTONS_DIS..
#> Up_5 REACTOME_MITOTIC_PRO.. KEGG_HUNTINGTONS_DIS.. KEGG_CELL_CYCLE
#> RAV695.Description RAV953.Description RAV1994.Description
#> <character> <character> <character>
#> Up_1 IRIS_Bcell-Memory_Ig.. IRIS_Bcell-Memory_Ig.. SVM T cells CD4 memo..
#> Up_2 DMAP_BCELLA3 IRIS_Bcell-Memory_IgM DMAP_TCELLA6
#> Up_3 IRIS_Bcell-naive IRIS_Bcell-naive DMAP_TCELLA8
#> Up_4 IRIS_Bcell-Memory_IgM DMAP_BCELLA3 DMAP_TCELLA2
#> Up_5 DMAP_BCELLA2 DMAP_BCELLA1 DMAP_TCELLA7
#> RAV312.Description RAV468.Description
#> <character> <character>
#> Up_1 REACTOME_CELL_CYCLE_.. REACTOME_METABOLISM_..
#> Up_2 REACTOME_MITOTIC_M_M.. NA
#> Up_3 REACTOME_DNA_REPLICA.. NA
#> Up_4 REACTOME_CELL_CYCLE NA
#> Up_5 NA NA
# only a specific RAV (note the colnames above)
subsetEnrichedPathways(miniRAVmodel,ind=695,n=5)
#> DataFrame with 5 rows and 1 column
#> RAV695.Description
#> <character>
#> Up_1 IRIS_Bcell-Memory_Ig..
#> Up_2 DMAP_BCELLA3
#> Up_3 IRIS_Bcell-naive
#> Up_4 IRIS_Bcell-Memory_IgM
#> Up_5 DMAP_BCELLA2