Markdown tables

Markdown tables

Usage

markdownTables(object, ...)

# S4 method for DFrameList
markdownTables(object, contrastName = NULL, n = 10L)

# S4 method for DESeqAnalysis
markdownTables(object, i, n = 10L)

# S4 method for DESeqResults
markdownTables(object, contrastName = NULL, n = 10L)

Arguments

object

Object.

contrastName

character(1) or NULL. Contrast name.

n

integer(1). Number of genes (per direction) to report.

i

Indices specifying elements to extract or replace. Indices are numeric or character vectors, empty (missing), or NULL.

For more information:

help(topic = "Extract", package = "base")

...

Additional arguments.

Value

kable. Markdown tables.

Note

Updated 2022-05-24.

Examples

data(deseq)

## DESeqAnalysis ====
markdownTables(deseq, i = 1L, n = 5L)
#> ℹ 30 differentially expressed genes (alpha < 0.01).
#> ℹ 17 upregulated genes (alpha < 0.01).
#> ℹ 13 downregulated genes (alpha < 0.01).
#> 
#> 
#> Table: condition_B_vs_A (upregulated)
#> 
#> |        | baseMean|lfc  |padj     |broadClass |geneName |description                                    |
#> |:-------|--------:|:----|:--------|:----------|:--------|:----------------------------------------------|
#> |gene65  |       61|2.40 |2.35e-04 |coding     |ARX      |aristaless related homeobox                    |
#> |gene202 |       49|2.46 |3.38e-04 |coding     |CAMK1G   |calcium/calmodulin dependent protein kinase IG |
#> |gene355 |       47|1.99 |7.47e-04 |coding     |CCDC88C  |coiled-coil domain containing 88C              |
#> |gene299 |       78|1.69 |1.93e-03 |coding     |WIZ      |WIZ zinc finger                                |
#> |gene80  |       55|1.87 |2.24e-03 |coding     |DHX33    |DEAH-box helicase 33                           |
#> 
#> 
#> Table: condition_B_vs_A (downregulated)
#> 
#> |        | baseMean|lfc   |padj     |broadClass |geneName |description                                        |
#> |:-------|--------:|:-----|:--------|:----------|:--------|:--------------------------------------------------|
#> |gene483 |       70|-2.61 |4.32e-08 |coding     |NUP160   |nucleoporin 160                                    |
#> |gene262 |       19|-4.60 |8.14e-06 |coding     |FUZ      |fuzzy planar cell polarity protein                 |
#> |gene434 |       39|-2.58 |8.73e-06 |coding     |STRAP    |serine/threonine kinase receptor associated pro... |
#> |gene478 |       64|-2.05 |1.97e-04 |coding     |ANK1     |ankyrin 1                                          |
#> |gene43  |       98|-1.82 |2.82e-04 |coding     |RBM5     |RNA binding motif protein 5                        |
#> |gene420 |       31|-2.31 |3.38e-04 |coding     |RNF10    |ring finger protein 10                             |
#> |gene467 |       52|-1.90 |8.34e-04 |coding     |SH2D2A   |SH2 domain containing 2A                           |
#> |gene219 |       40|-1.86 |6.61e-03 |coding     |CRY1     |cryptochrome circadian regulator 1                 |
#> |gene431 |       39|-1.49 |6.88e-03 |coding     |GLRX2    |glutaredoxin 2                                     |
#> |gene317 |       25|-1.79 |7.41e-03 |coding     |EXTL3    |exostosin like glycosyltransferase 3               |

## DESeqResults 'resultsTables()' return ====
res <- results(deseq, i = 1L)
resTbl <- resultsTables(res)
#> ℹ 30 differentially expressed genes (alpha < 0.01).
#> ℹ 17 upregulated genes (alpha < 0.01).
#> ℹ 13 downregulated genes (alpha < 0.01).
markdownTables(resTbl, n = 5L)
#> 
#> 
#> Table: upregulated
#> 
#> |        | baseMean|lfc  |padj     |
#> |:-------|--------:|:----|:--------|
#> |gene65  |       61|2.40 |2.35e-04 |
#> |gene202 |       49|2.46 |3.38e-04 |
#> |gene355 |       47|1.99 |7.47e-04 |
#> |gene299 |       78|1.69 |1.93e-03 |
#> |gene80  |       55|1.87 |2.24e-03 |
#> 
#> 
#> Table: downregulated
#> 
#> |        | baseMean|lfc   |padj     |
#> |:-------|--------:|:-----|:--------|
#> |gene483 |       70|-2.61 |4.32e-08 |
#> |gene262 |       19|-4.60 |8.14e-06 |
#> |gene434 |       39|-2.58 |8.73e-06 |
#> |gene478 |       64|-2.05 |1.97e-04 |
#> |gene43  |       98|-1.82 |2.82e-04 |
#> |gene420 |       31|-2.31 |3.38e-04 |
#> |gene467 |       52|-1.90 |8.34e-04 |
#> |gene219 |       40|-1.86 |6.61e-03 |
#> |gene431 |       39|-1.49 |6.88e-03 |
#> |gene317 |       25|-1.79 |7.41e-03 |