SurprisalAnalysis (version 3.0.0)

GO_analysis_surprisal_analysis: Perform Gene ontology analysis on a pattern of interest

Description

Perform Gene ontology analysis on a pattern of interest

Usage

GO_analysis_surprisal_analysis(
  transcript_weights,
  percentile_GO,
  lambda_no,
  key_type = "SYMBOL",
  flip = FALSE,
  species.db.str = "org.Hs.eg.db",
  ont = "BP",
  pAdjustMethod = "BH",
  top_GO_terms = 15
)

Value

dataframe, the important GO terms related to a lambda gene pattern

Arguments

transcript_weights

a dataframe containing the weight of transcripts in each pattern

percentile_GO

the percentile of transcript to be used for GO analysis, for example 95 will run GO on transcripts in the 95th percentile and above

lambda_no

the lambda pattern the user is interested in analyzing

key_type

type of transcripts which can be either SYMBOL, ENTREZID, ENSEMBL, or PROBEID

flip

a boolean variable which can either be true or false, if it is set to true, the lambda values will be multiplied by -1

species.db.str

the type of species used for GO analysis, by default set to Homo sapiens, can be either 'org.Hs.eg.db' or 'org.Mm.eg.db'

ont

the ontology term for GO enrichment analysis. Can be either "BP", "MF" or "CC". They stand for "Biological Process", "Molecular Function" or "Cellular Component". Set to "BP" by default

pAdjustMethod

multiple testing correction method. Could be one of "BH", "bonferroni", "holm", "hochberg", "hommel", "BY", or "none". The default setting is "BH"

top_GO_terms

number of GO terms returns, by default set to 15

Examples

csv.path <- system.file(
  "extdata", "helper_T_cell_0_test.csv",
  package = "SurprisalAnalysis"
)

expr.df <- utils::read.csv(csv.path, check.names = FALSE)
expr.df[1:700,]->expr.df
sa.res <- surprisal_analysis(expr.df, zero.handling = "log1p")
alph.all <- sa.res[[2]]

#In the example below, replace "none" with either 'org.Hs.eg.db' or 'org.Mm.eg.db'.
# \donttest{

go_top <- GO_analysis_surprisal_analysis(
    transcript_weights = alph.all,
    percentile_GO      = 99,
    lambda_no          = "lambda_1",
    key_type           = "SYMBOL",
    flip               = FALSE,
    species.db.str     = "none",
    ont                = "BP",
    pAdjustMethod      = "BH",
    top_GO_terms       = 15
    )
# }