flag_control_failures: Get control QA from an object returned by 'bactrl' or from an...

In ttriche/sesamizeGEO: the poor man's methylation suite (cf. `sesamizer`)

Get control QA from an object returned by bactrl or from an RGChannelSet

Description

Apply BeadArray thresholds for quality flagging. Thresholds obtained from the BeadArray Controls Reporter Software Guide (v00, source 2) and ewastools resource (v1.5, source 3). If an RGChannelSet is passed in, control_metrics() will be run on the rgSet and its detected annotation, then failures flagged.

Usage

flag_control_failures(rmat, dft = NULL, platform = "epic")

Arguments

rmat	return matrix from control_metrics(), or RGChannelSet
dft	optional threshold data.frame; defaults will be used if null
platform	optional platform indicator; will detect if rgSet ("EPIC")

Details

Every single EPIC IDAT that we have seen fails nonpolymorphic.grn and 99.5% of EPIC arrays fail bisulfite.conv.I.grn, so we mask these (for now) on EPIC. Zhou, Laird, and Shen (NAR 2017) document additional reasons why bisulfite conversion control probes on this platform are probably not informative, not least because poor bisulfite conversion will typically result in poor hybridization due to non-target cytosine bases in most probe oligos. In conclusion, these two control probe sets seem to be uninformative on EPIC, so they will be masked as NA if an EPIC rgSet is passed in.

Value

 an NxM matrix of threshold assessments, 0 = pass, 1 = fail

See Also

    control_metrics

Examples

if (exists("MPAL_rgSet")) {

  # TARGET MPAL data, from Alexander et al, Nature 2018
  flagged <- flag_control_failures(MPAL_rgSet)
  flagged <- flagged[apply(flagged, 1, function(x) !any(is.na(x))), ]
  all_samples <- ifelse(colSums(flagged, na.rm=TRUE) == 0, 
                        "all metrics pass", "some metrics fail")
  all_probes <- ifelse(rowSums(flagged, na.rm=TRUE) == 0, 
                       "all samples pass", "some samples fail")

  library(circlize)
  flagcols <- colorRamp2(c(0, 1), c("white", "darkred"))

  library(ComplexHeatmap)
  Heatmap(flagged, name="failed", col=flagcols, column_names_side="top",
          column_split=all_samples, column_names_gp=gpar(fontsize=8), 
          row_split=all_probes, row_names_side="left")

} 
  

ttriche/sesamizeGEO documentation built on Nov. 12, 2023, 5:42 p.m.