simple_goseq: Perform a simplified goseq analysis.

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Perform a simplified goseq analysis.

Description

goseq can be pretty difficult to get set up for non-supported organisms. This attempts to make that process a bit simpler as well as give some standard outputs which should be similar to those returned by clusterprofiler/topgo/gostats/gprofiler.

Usage

simple_goseq(
  sig_genes,
  go_db = NULL,
  length_db = NULL,
  doplot = TRUE,
  adjust = 0.1,
  threshold = 0.1,
  plot_title = NULL,
  length_keytype = "transcripts",
  go_keytype = "entrezid",
  goseq_method = "Wallenius",
  padjust_method = "BH",
  expand_categories = TRUE,
  excel = NULL,
  enrich = TRUE,
  minimum_interesting = 2,
  min_xref = 40,
  ...
)

Arguments

sig_genes	Data frame of differentially expressed genes, containing IDs etc.
go_db	Database of go to gene mappings (OrgDb/OrganismDb)
length_db	Database of gene lengths (gff/TxDb)
doplot	Include pwf plots?
adjust	Minimum adjusted pvalue for 'significant.'
threshold	Look at sets with this signficance or better.
plot_title	Set a title for the pvalue plots.
length_keytype	Keytype to provide to extract lengths
go_keytype	Keytype to provide to extract go IDs
goseq_method	Statistical test for goseq to use.
padjust_method	Which method to use to adjust the pvalues.
expand_categories	Expand the GO categories to make the results more readable?
excel	Print the results to an excel file?
enrich	Convert the goseq result to the clusterProfiler format?
minimum_interesting	Exclude categories with less than this number of genes.
min_xref	Stop everything if we get less than this intersection of genes/GO/lengths.
...	Extra parameters which I do not recall

Value

Big list including: the pwd:pwf function, alldata:the godata dataframe, pvalue_histogram:p-value histograms, godata_interesting:the ontology information of the enhanced groups, term_table:the goterms with some information about them, mf_subset:a plot of the MF enhanced groups, mfp_plot:the pvalues of the MF group, bp_subset:a plot of the BP enhanced groups, bpp_plot, cc_subset, and ccp_plot

See Also

[goseq] [GO.db] [GenomicFeatures] [stats::p.adjust()]

Examples

## Not run: 
 lotsotables <- simple_goseq(gene_list, godb, lengthdb)

## End(Not run)

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