Results — results • AcidGSEA

Results

Usage

results(object, ...)

# S4 method for FgseaList
results(object, contrast, collection)

Arguments

object: Object.
contrast: character(1). Contrast name.
collection: character(1). Gene set collection name. Typically refers to h (hallmark), c1-c7 collections from MSigDb. Can obtain using collectionNames() on FgseaList object.
...: Additional arguments.

Value

Varies, depending on the method.

Note

Updated 2022-04-27.

Examples

data(fgsea)

## FgseaList ====
object <- fgsea
contrast <- contrastNames(object)[[1L]]
collection <- collectionNames(object)[[1L]]
results(
    object = fgsea,
    contrast = contrast,
    collection = collection
)
#> DataFrame with 49 rows and 8 columns
#>                    pathway      pval      padj   log2err        es       nes
#>                <character> <numeric> <numeric> <numeric> <numeric> <numeric>
#> 1    HALLMARK_ADIPOGENESIS 0.7962185  0.985767 0.0584693 -0.281399 -0.748067
#> 2   HALLMARK_ALLOGRAFT_R.. 0.7356322  0.985767 0.0578530  0.281639  0.811042
#> 3   HALLMARK_ANDROGEN_RE.. 0.2213884  0.985767 0.1250334  0.549773  1.255340
#> 4    HALLMARK_ANGIOGENESIS 0.0700758  0.731343 0.2343926  0.884336  1.333084
#> 5   HALLMARK_APICAL_JUNC.. 0.9474790  0.985767 0.0503964 -0.197609 -0.627792
#> ...                    ...       ...       ...       ...       ...       ...
#> 45  HALLMARK_UNFOLDED_PR..  0.908068  0.985767 0.0471642  0.271914  0.620884
#> 46  HALLMARK_UV_RESPONSE..  0.322176  0.985767 0.1071402 -0.407273 -1.118379
#> 47  HALLMARK_UV_RESPONSE..  0.933902  0.985767 0.0517405 -0.259448 -0.602410
#> 48  HALLMARK_WNT_BETA_CA..  0.719409  0.985767 0.0635008 -0.576065 -0.860950
#> 49  HALLMARK_XENOBIOTIC_..  0.277083  0.985767 0.1167392 -0.395074 -1.144099
#>          size            leadingEdge
#>     <integer>            <character>
#> 1          12       ADIPOR2, NDUFAB1
#> 2          16         CD4, FGR, CD74
#> 3           8 ELOVL5, RRP12, PLPP1..
#> 4           2          VCAN, PGLYRP1
#> 5          21 ITGA3, SKAP2, CNTN1,..
#> ...       ...                    ...
#> 45          8    MTREX, MTHFD2, NFYA
#> 46         13   CELF2, CDON, COL11A1
#> 47          8                   FMO1
#> 48          2             DVL2, CUL1
#> 49         16 ITIH4, GCLC, FMO1, F..