Top tables of significantly enriched pathways.

topTables(object, ...)

# S4 method for FGSEAList
topTables(object, collection, n = 10L,
  headerLevel = 3L)

Arguments

object

Object.

collection

character(1). Gene set collection name. Typically refers to h, c1-c7 collections from MSigDb. Can obtain using collectionNames() on FGSEAList object.

n

integer(1). Number of significant processes to include. Bidirectional; will include n up- and down-regulated processes.

headerLevel

integer(1). Markdown header level.

...

Additional arguments.

Value

Markdown output.

Details

Supports looping across multiple DEG results, and adds a Markdown header for each contrast.

Examples

data(gsea) topTables(gsea, collection = "h")
#> #> #> ### dmso_r1881_vs_etoh #> #> #> #> #### Upregulated #> #> #> #> |pathway | padj| NES| size| #> |:----------------------------------|-----:|-----:|----:| #> |HALLMARK_E2F_TARGETS | 0.005| 3.111| 196| #> |HALLMARK_MYC_TARGETS_V1 | 0.005| 2.814| 197| #> |HALLMARK_ANDROGEN_RESPONSE | 0.005| 2.743| 97| #> |HALLMARK_G2M_CHECKPOINT | 0.005| 2.723| 193| #> |HALLMARK_MYC_TARGETS_V2 | 0.005| 2.452| 58| #> |HALLMARK_MTORC1_SIGNALING | 0.005| 2.375| 197| #> |HALLMARK_DNA_REPAIR | 0.005| 2.229| 140| #> |HALLMARK_UNFOLDED_PROTEIN_RESPONSE | 0.005| 1.929| 107| #> |HALLMARK_MITOTIC_SPINDLE | 0.005| 1.875| 197| #> |HALLMARK_ESTROGEN_RESPONSE_LATE | 0.005| 1.875| 192| #> #> #> #### Downregulated #> #> #> #> |pathway | padj| NES| size| #> |:----------------------------------|-----:|------:|----:| #> |HALLMARK_INTERFERON_ALPHA_RESPONSE | 0.012| -1.549| 91| #> |HALLMARK_MYOGENESIS | 0.014| -1.830| 181| #> |HALLMARK_HEDGEHOG_SIGNALING | 0.014| -1.778| 34| #> |HALLMARK_HEME_METABOLISM | 0.014| -1.515| 187| #> |HALLMARK_COAGULATION | 0.019| -1.499| 118| #> |HALLMARK_UV_RESPONSE_DN | 0.021| -1.554| 137| #> |HALLMARK_COMPLEMENT | 0.022| -1.485| 180| #> |HALLMARK_APICAL_JUNCTION | 0.022| -1.427| 187|