annotatedEnh2Exprs: Compute expression methylation correlation

In GianlucaMattei/methyl.O: Annotate, Score and Visualize Differentially Methylated Regions

Compute expression methylation correlation

Description

Compute and plot correlation between expression and methylation

Usage

annotatedEnh2Exprs(
  annotatedEnhancers,
  expressionProfile,
  hg = "hg19",
  enhancer.db = "FANTOM5",
  col.genes = 0,
  col.stat = 6,
  stat.thr = 0.05,
  col.logFC = 2,
  logfc.thr = 0.5,
  convert.genes = FALSE,
  convert.from,
  beta.thr = 0.3,
  overlap.param.thr = 40,
  param.type = "overlap.percentage",
  line.col = "lightgrey",
  lmfit.col1 = "red",
  lmfit.col2 = "green",
  pal = "RdGy",
  plot.type = "splitted",
  show.text = FALSE,
  cor.type = "pearson",
  return.table = FALSE
)

Arguments

annotatedEnhancers	data.frame. It corresponds to resulting list from annotateEnhancers()
expressionProfile	expression profile data.frame
hg	character, "hg19", "hg38". Version of the enhancer database. Default = "hg19"
enhancer.db	character, which database to use between 'FANTOM5' or '4DGenome'. Default = "FANTOM5"
col.genes	numeric, the column of expressionProfile data.frame with gene Ids. If NULL geneIDs will be taken from rownames() of expressionProfile. Default = 0.
col.stat	numeric, the column of expressionProfile data.frame with the statistics to use. Default = 6.
stat.thr	threshold for statistical significance. Default = 0.05
col.logFC	numeric, the column of expressionProfile data.frame with log. fold change. Default = 2
logfc.thr	numeric, threshold value for log. fold change. Default = 0.
convert.genes	logical, used to indicate if gene ids have to be translated in official gene symbols. Default = FALSE
convert.from	character, used annotation for gene in expressionProfile to be converted to symbols gene IDs. Accepted: c("ENTREZID" ,"EXONID" ,"GENEBIOTYPE" ,"GENEID" ,"GENENAME" ,"PROTDOMID" ,"PROTEINDOMAINID" ,"PROTEINDOMAINSOURCE" ,"PROTEINID" ,""SEQSTRAND" ,"SYMBOL" ,"TXBIOTYPE" ,"TXID" ,"TXNAME" ,"UNIPROTID")
beta.thr	numeric, beta difference threshold value. Default = 0.3.
overlap.param.thr	numeric, threshold value for selected parameter to filter methylations overlapping the selected features. Default = 100
param.type	character, threshold parameter to filter methylations overlapping the selected features. Accetped c("dmr.length", "overlap.length", "overlap.percentage"). Default = "overlap.length".
line.col	character, color of lines at x=0, y=0. Defalt = "lightgray"
lmfit.col1	character, color of linear model line 1 or for simple plot. Defalt = "red"
lmfit.col2	character, color of linear model line 2. Defalt = "green"
pal	character, color palette. hcl.pals() to show available. Default = "RdGy"
plot.type	character, compute or not different linear models for upregulated and downregulated genes. Accepted: "simple" or "splitted". Default = "splitted".
show.text	logical, indicating if print gene names in the final plot. Accepted values: TRUE or FALSE. Default = FALSE.
cor.type	character, correlation method. Available "pearson", "kendall" or "spearman" correlation, Default = "pearson"
return.table	logical, TRUE return a data.frame instead a plot. Default = FALSE

Value

plot of correlation or (if return.table = TRUE) a data.frame of genes expression associated to beta methylation values of enhancers.

GianlucaMattei/methyl.O documentation built on Sept. 12, 2023, 11:53 p.m.