heatmapPairs {ELMER} | R Documentation |
Heatmp plot of pairs gene and probes anti-correlated
heatmapPairs( data, group.col, group1, group2, pairs, subset = FALSE, cluster.within.groups = TRUE, plot.distNearestTSS = FALSE, annotation.col = NULL, met.metadata = NULL, exp.metadata = NULL, width = 10, height = 7, filename = NULL )
data |
A MultiAssayExperiment with a DNA methylation SummarizedExperiment (all probes) and a gene Expression SummarizedExperiment. |
group.col |
A column from the sample matrix from the MultiAssayExperiment object. Accessed with colData(mae) |
group1 |
A group from group.col. ELMER will run group1 vs group2. That means, if direction is hyper, get probes hypermethylated in group 1 compared to group 2. |
group2 |
A group from group.col. ELMER will run group1 vs group2. That means, if direction is hyper, get probes hypermethylated in group 1 compared to group 2. |
pairs |
List of probe and pair genes |
subset |
Subset MAE object to keep only groups compared ? |
cluster.within.groups |
Cluster columns based on the groups |
plot.distNearestTSS |
Plot track with distNearestTSS ? |
annotation.col |
A vector of columns from the sample matrix from the MultiAssayExperiment object. Accessed with colData(mae) to be added as annotation to the heatmap. |
met.metadata |
A vector of metdatada columns available in the DNA methylation GRanges to should be added to the heatmap. |
exp.metadata |
A vector of metdatada columns available in the Gene expression GRanges to should be added to the heatmap. |
width |
Figure width |
height |
Figure height |
filename |
File names (.pdf) to save the file (i.e. "plot.pdf"). If NULL return plot. |
A heatmap
Tiago Chedraoui Silva (tiagochst at gmail.com)
## Not run: data <- ELMER:::getdata("elmer.data.example") group.col <- "subtype_Expression.Subtype" group1 <- "classical" group2 <- "secretory" pairs <- data.frame(Probe = c("cg15924102","cg19403323", "cg22396959"), GeneID = c("ENSG00000196878", "ENSG00000009790", "ENSG00000009790" ), Symbol = c("TRAF3IP3","LAMB3","LAMB3"), Distance = c(6017,168499,0), Raw.p = c(0.001,0.00001,0.001), Pe = c(0.001,0.00001,0.001)) heatmapPairs(data = data, group.col = group.col, group1 = group1, group2 = group2, annotation.col = c("ethnicity","vital_status","age_at_diagnosis"), pairs, filename = "heatmap.pdf") ## End(Not run)