annotatedDMRs2Exprs: Compute correlation between expression and methylation...

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

Compute correlation between expression and methylation levels.

Description

Compute correlation between expression and methylation levels.

Usage

annotatedDMRs2Exprs(
  annotatedDMRs,
  expressionProfile,
  active.features = c("promoters", "heads"),
  col.genes = 0,
  col.stat = 6,
  stat.thr = 0.05,
  col.logFC = 2,
  logfc.thr = 0,
  convert.genes = FALSE,
  convert.from,
  beta.thr = 0.3,
  overlap.param.thr = 100,
  param.type = "overlap.length",
  line.col = "lightgrey",
  lmfit.col1 = "red",
  lmfit.col2 = "green",
  pal = "RdGy",
  plot.type = "splitted",
  show.text = FALSE,
  cor.type = "pearson",
  filter.by.genes = NULL,
  return.table = FALSE
)

Arguments

annotatedDMRs	anotated DMRs list resultingfrom annotateDMRs() or scoreAnnotatedDMRs()
expressionProfile	data.frame, expression profile.
active.features	character vectors, containing features to correlate. Must be from names of resulting list from annotateDMRs. Additional feature names can be first exons (exons1) or first intron (intron1). To use more than one feature use c(). Default = c("promoters", "heads")
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	numeric, 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	boolean, 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	nuemric, 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. Default = "lightgray"
lmfit.col1	character, color of linear model line 1 or for simple plot. Default = "red"
lmfit.col2	character, color of linear model line 2. Default = "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"
filter.by.genes	character vectors, gene symbols used for filtering output
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.

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