metadeconfoundR (version 1.0.5)

ImportLongPrior: ImportLongPrior

Description

ImportLongPrior imports prior knowledge of associations between individual features and metadata in form of a long-format dataframe.

Usage

ImportLongPrior(longPrior, featureMat, metaMat)

Value

wide-format dataframe that can be used as minQValues parameter in MetaDeconfound

Arguments

longPrior

long-format dataframe as generated by Metadeconfound(returnLong = TRUE). Must contain at least one column containing feature names and one column containing associated metadata names, called "feature" and "metaVariable", respectively. Only associations between features and metadata present in featureMat and metaMat will be returned. Additionally, "Qs" and "status" (as produced by MetaDeconfound)columns can be supplied and will be parsed as well. If only "feature" and "metaVariable" columns are supplied, all listed associations are assumed to be significant. If "status" is supplied, only non-"NS" labeled associations will be kept.

featureMat

omics features to be analyzed by MetaDeconfound

metaMat

metadata to be analyzed by MetaDeconfound

Details

This function is meant to facilitate incorporation of prior knowledge about associations between measured omics features and available metadata both from earlier metadeconfoundR runs by supplying the long-format Metadeconfound(returnLong = TRUE) output directly or by supplying a simple list of known associations from other studies.

Examples

data(reduced_feature)
data(metaMatMetformin)
# \donttest{

# note that this example is only to demonstrate the process of integrating
 # prior knowledge into a MetaDeconfound() analysis. Using the output of a
 # MetaDeconfound() run as minQValues input for a second run with the exact
 # same features and metadata will not lead to any new insights since the set
 # of QValues calculated by MetaDeconfound() and the set supplied using the
 # minQValues parameter are identical in this case.

example_output <- MetaDeconfound(featureMat = reduced_feature,
                                  metaMat = metaMatMetformin,
                                  returnLong = TRUE,
                                  logLevel = "ERROR")

minQValues <- ImportLongPrior(longPrior = example_output,
                                featureMat = reduced_feature,
                                metaMat = metaMatMetformin)

example_output2 <- MetaDeconfound(featureMat = reduced_feature,
                                  metaMat = metaMatMetformin,
                                  minQValues = minQValues,
                                  logLevel = "ERROR")
# }