hpgltools: A pile of (hopefully) useful R functions

combine_de_tables

R 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.

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 April 8, 2024, 1:30 a.m.