module_ge: module_ge

In oriolarques/GEGVIC: A workflow to analyse Gene Expression, Genetic Variations and Immune cell Composition of tumour samples using Next Generation Sequencing data.

module_ge

Description

Analyses differential gene expression from RNA-seq raw counts and plots PCA, volcano plots and gene set enrichment analysis (GSEA) for the desired comparisons. This last analysis include also Gene Set Variation Analysis.

Usage

module_ge(
  counts,
  genes_id,
  metadata,
  response,
  design,
  colors = c("orange", "black"),
  ref_level,
  shrink = "apeglm",
  biomart,
  fold_change = 2,
  p.adj = 0.05,
  gmt,
  gsea_pvalue = 0.2,
  gsva_gmt = "hallmark",
  kcdf = "Gaussian",
  method = "gsva",
  row.names = TRUE,
  col.names = TRUE
)

Arguments

counts	Data frame that contains gene expression data as raw counts.
genes_id	Name of the column that contains gene identifiers. Should be one of the following:'entrez_gene_id', 'ensemblgene_id' or 'hgnc_symbol'.
metadata	Data frame that contains supporting variables to the data.
response	Unquoted name of the variable indicating the groups to analyse.
design	Variables in the design formula in the form of: 'Var1 + Var2 + ... Var_n'.
colors	Character vector indicating the colors of the different groups to compare. Default values are two: black and orange.
ref_level	Character vector where the first element is the column name where the reference level is located and a second element indicating the name of level to be used as a reference when calculating differential gene expression.
shrink	Name of the shrinkage method to apply: "apeglm", "ashr", "normal" or "none". Use none to skip shrinkage. Default value is "apeglm".
biomart	Data frame containing a biomaRt query with the following attributes: ensembl_gene_id, hgnc_symbol, entrezgene_id, transcript_length, refseq_mrna. In the case of mus musculus data, external_gene_name must be obtained and then change the column name for hgnc_symbol. Uploaded biomaRt queries in GEGVIC: 'ensembl_biomartGRCh37', ensembl_biomartGRCh38_p13' and 'ensembl_biomartGRCm38_p6', 'ensembl_biomartGRCm39'.
fold_change	An integer to define the fold change value to consider that a gene is differentially expressed.
p.adj	Numeric value to define the maximum adjusted p-value to consider that a gene is differentially expressed.
gmt	A data frame containg the gene sets to analyse using GSEA. This object should be obtained with the read.gmt function from the clusterProfiler package.
gsea_pvalue	Numeric value to define the adjusted pvalue cutoff during GSEA. Set to 0.2 by default.
gsva_gmt	Path to the gmt file that contain the gene sets of interest. By default the parameter is set to 'hallmark' which provides all HALLMARK gene sets from MSigDB (version 7.5.1).
kcdf	Character string denoting the kernel to use during the non-parametric estimation of the cumulative distribution function of expression levels across samples when method="gsva". By default, "Gaussian" since GEGVIC transforms raw counts using the vst transformation. Other options are 'Poisson' or 'none'.
method	Name of the method to perform Gene set variation analysis. The options are: 'gsva', 'ssgea' or 'zscore'. Default value is 'gsva'.
row.names	Logical value to determine if row-names are shown in the heatmap.
col.names	Logical value to determine if column-names are shown in the heatmap.

Value

Returns ggplot objects (containing PCA, Volcano plot and GSEA analyses) and a list of data frames containing the results data.

Examples

tables_module_ge <- module_ge(counts = sample_counts,
                              genes_id = 'ensembl_gene_id',
                              metadata = sample_metadata,
                              response = MSI_status,
                              design = 'MSI_status',
                              colors = c('orange', 'black'),
                              ref_level = c('MSI_status', 'MSS'),
                              shrink = 'apeglm',
                              biomart = ensembl_biomart_GRCh38_p13,
                              fold_change = 2,
                              p.adj = 0.05,
                              gmt = 'inst/extdata/c2.cp.reactome.v7.5.1.symbols.gmt',
                              gsea_pvalue = 0.2,
                              gsva_gmt = 'hallmark',
                              method = 'gsva',
                              kcdf = 'Gaussian',
                              row.names = TRUE,
                              col.names = TRUE)

oriolarques/GEGVIC documentation built on Oct. 30, 2024, 10:44 p.m.