Biological signal reduction

Reduce biological signal by decreasing the mean group difference between sample groups.

Usage

reduce.signal(
  biological.effect,
  group.id,
  group.id.level = c("E", "V"),
  reduce.multiplier = 1/2,
  pbset.id = NULL
)

Arguments

biological.effect

the estimated biological effect dataset. The dataset must have rows as probes and columns as samples. It can only take in probe-level dataset with a fixed number of probes per unique probe-set.

group.id

a vector of sample-group labels for each sample of the estimated biological effect dataset.

group.id.level

a vector of sample-group label level. It must have two and only two elements and the first element is the reference. By default, group.id.level = c("E", "V"). That is in our study, we compare endometrial tumor samples to ovarian tumor samples, with endometrial as our reference.

reduce.multiplier

a multiplier specified to reduce between-sample-group signal by. By default, reduce.multiplier = 1/2.

pbset.id

a vector of unique probe-set names. If it is not specified, it is the unique probe names of the dataset, extracting from the row names.

Value

estimated biological effect data, with reduced biological signal

Examples

biological.effect <- estimate.biological.effect(uhdata = uhdata.pl)
handling.effect <- estimate.handling.effect(uhdata = uhdata.pl,
                             nuhdata = nuhdata.pl)

ctrl.genes <- unique(rownames(uhdata.pl))[grep("NC", unique(rownames(uhdata.pl)))]

biological.effect.nc <- biological.effect[!rownames(biological.effect) %in% ctrl.genes, ]
handling.effect.nc <- handling.effect[!rownames(handling.effect) %in% ctrl.genes, ]
group.id <- substr(colnames(biological.effect.nc), 7, 7)

redhalf.biological.effect.nc <- reduce.signal(biological.effect = biological.effect.nc,
                                    group.id = group.id,
                                    group.id.level = c("E", "V"),
                                    reduce.multiplier = 1/2)