gene_enrichment_GO: This function carries out a GO enrichment analysis between a...

In Single-Cell-Genomics-Group-CNAG-CRG/SCrafty-package: R package to store useful functions to analyze single-cell data that the entire team can benefit

This function carries out a GO enrichment analysis between a set of differentially expressed genes within the specified gene universe.

Description

This function carries out a GO enrichment analysis between a set of differentially expressed genes within the specified gene universe.

Usage

gene_enrichment_GO(
  gene_de,
  gene_universe,
  gene_from = "SYMBOL",
  gene_to = "ENTREZID",
  pvalue_cutoff = 0.05,
  test_direction = "over",
  annotation = "org.Hs.eg.db",
  ontology = "BP"
)

Arguments

gene_de	Vector of gene symbols or ensemble identifiers we want to test.
gene_universe	Vector of gene symbols or ensemble identifiers constituting the entire gene universe to test, rownames(se_obj).
gene_from	Character string specifying the gene identifier is gene_vec, By default SYMBOL, can also be ENTREZID, ENSEMBL, UNIGENE
gene_to	Character string specifying what the gene id we want to convert the gene_vec to. By default ENTREZID, can also be SYMBOL, ENSEMBL, UNIGENE
pvalue_cutoff	Cutoff to use for the Pvalue
test_direction	Character string which can be either "over" or "under". This determines whether the test performed detects over or under represented GO terms.
annotation	Character string specifying specifying the annotation of the organism to use. By default human org.Hs.eg.db but you can also choose mouse org.Mm.eg.db.
ontology	which ontology do we want to test BP (biological processes), CC (cellular component), or MF (molecular function)

Value

Named vector with ENTREZID as the values.

Examples

## Not run: 
  gene_de <- c("MS4A1", "CD79A", "CD79B")
  gene_universe <- c("HLA-DRA", "AIF1", "C1QA", "LYZ", "SELENOP", "ADAMDEC1",
  "CD14", "CD68", "IGF1", "LGMN", "AXL", "C5AR1", "CD163", "CD163L1",
  "CD209", "CSF1R", "IL10", "IL10RA", "IL13RA1", "NRP1", "NRP2", "SDC3",
  "TGFBI", "TGFBR1", "EEF1A1", "OAZ1", "RPL15", "RPL19", "RPS19", "RPS29",
  "TPT1", "UBA52", "APOE", "FCGRT", "MKI67", "PCLAF", "RRM2", "CD1C", "CLC",
  "IL4", "TPSAB1", "CPA3", "NRG1", "RETN", "EREG", "ACOD1", "TNIP3", "VCAN",
  "INHBA", "CXCL5", "HTRA1", "SPP1", "HSPA1B", "CXCR2", "PI3", "PROK2",
  "HSPA6", "NCCRP1", "LAD1", "CCL22", "MS4A1", "CD79A", "CD79B", "SIGLEC1")

  GO_results <- gene_enrichment_GO(
  gene_de = gene_de,
  gene_universe = gene_universe,
  gene_type = "SYMBOL",
  annotation = "org.Hs.eg.db",
  pvalue_cutoff = 0.05,
  test_direction = "over",
  ontology = "BP")

## End(Not run)

Single-Cell-Genomics-Group-CNAG-CRG/SCrafty-package documentation built on Aug. 20, 2022, 9:29 a.m.