goseq_msigdb: Pass MSigDB categorical data to goseq and run it.

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

Pass MSigDB categorical data to goseq and run it.

Description

goseq is probably the easiest method to push varying data types into. Thus it was the first thing I thought of when looking to push MSigDB data into a GSEA method.

Usage

goseq_msigdb(
  sig_genes,
  signatures = "c2BroadSets",
  data_pkg = "GSVAdata",
  signature_category = "c2",
  current_id = "ENSEMBL",
  required_id = "ENTREZID",
  length_db = NULL,
  doplot = TRUE,
  adjust = 0.1,
  pvalue = 0.1,
  length_keytype = "transcripts",
  go_keytype = "entrezid",
  goseq_method = "Wallenius",
  padjust_method = "BH",
  excel = NULL,
  orgdb = "org.Hs.eg.db"
)

Arguments

sig_genes	Character list of genes deemed significant. I think in the current implementation this must be just a list of IDs as opposed to the full dataframe of interesting genes because we likely need to convert IDs.
signatures	Used by load_gmt_signatures(), the signature file or set.
data_pkg	Used by load_gmt_signatures().
signature_category	Ibid, but the name of the signatures group.
current_id	Used by convert_msig_ids(), when converting IDs, the name of the existing type.
required_id	What type to convert to in convert_msig_ids().
length_db	Dataframe of lengths. It is worth noting that goseq explicitly states that one might wish to use other potentially confounding factors here, but they only examine lenghts in their paper. Starting with this parameter, everything is just passed directly to simple_goseq()
doplot	Print the prior plot?
adjust	passed to simple_goseq()
pvalue	passed to simple_goseq()
length_keytype	passed to simple_goseq()
go_keytype	passed to simple_goseq()
goseq_method	passed to simple_goseq()
padjust_method	passed to simple_goseq()
excel	passed to simple_goseq()
orgdb	Ideally used to help goseq collect lengths.

Value

Some goseq data!

See Also

[gsva] [goseq]

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