combine_de_tables: Combine portions of deseq/limma/edger table output.

View source: R/de_xlsx.R

combine_de_tablesR Documentation

Combine portions of deseq/limma/edger table output.

Description

This hopefully makes it easy to compare the outputs from limma/DESeq2/EdgeR on a table-by-table basis.

Usage

combine_de_tables(
  apr,
  extra_annot = NULL,
  keepers = "all",
  excludes = NULL,
  adjp = TRUE,
  include_limma = TRUE,
  include_deseq = TRUE,
  include_edger = TRUE,
  include_ebseq = TRUE,
  include_basic = TRUE,
  include_noiseq = TRUE,
  include_dream = FALSE,
  rownames = TRUE,
  add_plots = TRUE,
  loess = FALSE,
  plot_dim = 6,
  compare_plots = TRUE,
  padj_type = "fdr",
  fancy = FALSE,
  lfc_cutoff = 1,
  p_cutoff = 0.05,
  de_types = c("limma", "deseq", "edger"),
  excel_title = "Table SXXX: Combined Differential Expression of YYY",
  increment_start = "SXXX",
  start_worksheet_num = 2,
  rda = NULL,
  rda_input = FALSE,
  label = 10,
  label_column = "hgncsymbol",
  format_sig = 4,
  excel = NULL,
  plot_columns = 10,
  alpha = 0.4,
  z = 1.5,
  z_lines = FALSE
)

Arguments

apr

Output from all_pairwise().

extra_annot

Add some annotation information?

keepers

List of reformatted table names to explicitly keep certain contrasts in specific orders and orientations.

excludes

List of columns and patterns to use for excluding genes.

adjp

Perhaps you do not want the adjusted p-values for plotting?

include_limma

Include limma analyses in the table?

include_deseq

Include deseq analyses in the table?

include_edger

Include edger analyses in the table?

include_ebseq

Include ebseq analyses in the table?

include_basic

Include my stupid basic logFC tables?

include_noiseq

Include results from NoiSeq?

include_dream

Include results from the variancePartition 'dream' method?

rownames

Add rownames to the xlsx printed table?

add_plots

Add plots to the end of the sheets with expression values?

loess

Add time intensive loess estimation to plots?

plot_dim

Number of inches squared for the plot if added.

compare_plots

Add some plots comparing the results.

padj_type

Add a consistent p adjustment of this type.

fancy

Save a set of fancy plots along with the xlsx file?

lfc_cutoff

In this context, only used for plotting volcano/MA plots.

p_cutoff

In this context, used for volcano/MA plots.

de_types

Used for plotting pvalue/logFC cutoffs.

excel_title

Title for the excel sheet(s). If it has the string 'YYY', that will be replaced by the contrast name.

increment_start

When incrementing the table number for each contrast, look for this string and increment when it is found. It should therefore be found in the excel_title.

start_worksheet_num

Start writing data at this worksheet number. (in case you want to put other stuff in)

rda

Write a rda file of the results.

rda_input

Include the input all_pairwise() result in the rda?

label

Label this number of top-n genes on the plots?

label_column

Use this gene annotation column to pick up gene labels.

format_sig

Use this many significant digits for printing wacky numbers.

excel

Filename for the excel workbook, or null if not printed.

plot_columns

A guesstimate of how wide plots are with respect to 'normally' sized columns in excel.

alpha

Use the alpha channel with this transparency when plotting.

z

Use this z-score for defining significant in coefficient plots.

z_lines

Add z-score lines to coefficient plots?

Value

Table combining limma/edger/deseq outputs.

See Also

[all_pairwise()] [extract_significant_genes()]

Examples

## Not run: 
 expt <- create_expt(metadata="some_metadata.xlsx", gene_info=funkytown)
 big_result <- all_pairwise(expt, model_batch=FALSE)
 pretty <- combine_de_tables(big_result, table='t12_vs_t0')
 pretty <- combine_de_tables(big_result, table='t12_vs_t0',
                             keepers=list("avsb"=c("a","b")))
 pretty <- combine_de_tables(big_result, table='t12_vs_t0',
                             keepers=list("avsb"=c("a","b")),
                             excludes=list("description"=c("sno","rRNA")))

## End(Not run)

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.