Run the improved Houseman method

Run the improved Houseman method

Usage

run_flowsortedblood(
  methyl_set,
  array = c("450k", "EPIC"),
  compositeCellType = c("Blood", "CordBloodCombined", "CordBlood", "CordBloodNorway",
    "CordTissueAndBlood", "DLPFC"),
  processMethod = "preprocessQuantile",
  probeSelect = c("IDOL", "both", "any"),
  cellTypes = c("CD8T", "CD4T", "NK", "Bcell", "Mono", "Neu"),
  referencePlatform = c("IlluminaHumanMethylationEPIC", "IlluminaHumanMethylation450k",
    "IlluminaHumanMethylation27k"),
  referenceset = NULL,
  CustomCpGs = NULL,
  meanPlot = FALSE,
  verbose = TRUE,
  lessThanOne = FALSE,
  cellCounts = NULL,
  ...
)

Arguments

methyl_set

A minfi MethylSet

array

type of methylation array that was used. possible options are '450k' and 'EPIC'

compositeCellType

Which composite cell type is being deconvoluted. Should be one of "Blood", "CordBloodCombined", "CordBlood", "CordBloodNorway", "CordTissueAndBlood", or "DLPFC". See details for preferred approaches.

processMethod

Joint normalization/background correction for user and reference data. For MethylSet objects only "preprocessQuantile" is available. Set it to any minfi preprocessing function as a character if you want to override it, like "preprocessFunnorm"

probeSelect

How should probes be selected to distinguish cell types? Options include: 1) "IDOL", (default) for using a customized set of probes obtained from IDOL optimization, available for Blood and Umbilical Cord Blood 2) "both", which selects an equal number (50) of probes (with F-stat p-value < 1E-8) with the greatest magnitude of effect from the hyper- and hypo-methylated sides, and 3) "any", which selects the 100 probes (with F-stat p-value < 1E-8) with the greatest magnitude of difference regardless of direction of effect. This according to minfi algorithm. Default input "auto" in minfi will use "any" for cord blood and "both" otherwise. Please see references for more details.

cellTypes

A vector of length K that contains the cell type names. Default: c("CD8T", "CD4T", "NK", "Bcell", "Mono", "Neu"). Please notice that this library use Neutrophils instead of Granulocytes. See details for your library.

referencePlatform

The platform for the reference dataset; options include c("IlluminaHumanMethylation450k", "IlluminaHumanMethylationEPIC" (default), "IlluminaHumanMethylation27k"). If the input rgSet belongs to another platform, it will be converted using minfi function convertArray. Should not be changed by the user.

referenceset

It is NULL by default. A custom reference RGChannelSet object (in quotes) if it is not a package installed. This option also allows the user to perform the deconvolution in closed computing clusters without internet access to ExperimentHub. For that download and save the reference and input the resulting object here. If using an installed reference package set to NULL.

CustomCpGs

a custom vector of probe names for cell deconvolution. For custom lists it should be a vector object (no quotes).

meanPlot

Whether to plots the average DNA methylation across the cell-type discriminating probes within the mixed and sorted samples.

verbose

Should the function be verbose?

lessThanOne

Should the predictions be constrained to exactly one, in minfi default is FALSE, now you can select the option

cellCounts

If cell counts are available (CBC, of flow sort) add a vector of lenght equal to the samples being deconvolved

...

Other arguments for preprocessquantile or other normalizations

returnAll

Should the composition table and the normalized user supplied data be return? Default is False.