extractMarkers. CellMix 1.6

Description

When expression data from pure samples are available, it is possible to select genes for their ability to discriminate between the different cell-types. The function extractMarkers provides an interface to compute scores or statistics using different methods, and select the ones that pass a given threshold.

For long-runnning scoring methods, the marker selection process could be performed manually, by separating the scoring and selections steps, e.g.: sc <- scoreMarkers(eset, data=groups, method='HSD') selectMarkers(sc, threshold=10^-3)

markerScoreMethod defines/retrieves marker scoring methods.

Usage

extractMarkers(object, ...)

S4 (ANY)
`extractMarkers`(object, data = NULL, method = "Abbas", threshold = NA, 
  decreasing = FALSE, ..., format = c("list", "raw"))

scoreMarkers(...)

markerScoreMethod(method, object, ...)

Arguments

object: A numeric matrix, an object of class ExpressionSet, or a MarkerList-class object.
data: main extra data used by the scoring and selection methods. If object is a matrix-like object, data is generally a factor or grouping variable, as a vector, that defines the cell-type for each -- pure -- sample. If a vector, this argument is converted into a factor with the levels in their order of appearance in data, by factor(data, levels=unique(data)). This is to obtain levels in an order that is consistent with the samples' order. If object is a MarkerList object, then data is generally a matrix-like object that contains expression data.
method: accession key of the method either used to compute marker scores in extractMarkers, or to define/retrieve scoring methods in markerScoreMethod. All available methods can be retrieved via markerScoreMethod(). A custom scoring method can also be passed as a function.
...: other parameters passed to the scoring method in extractMarkers and selectMarkers, or that define default arguments when defining a scoring method with markerScoreMethod.
format: specifies the output format: ‘list’ returns a MarkerList-class object and ‘raw’ directly returns the result of the scoring method -- which can be useful for lengthy computations.
threshold: threshold that is applied to filter markers based on their respective statistic/score: Genes with statistic >= threshold are selected if decreasing=TRUE. Otherwise, if decreasing=FALSE or NA, the selected genes are those with statistic <= threshold. Filtering is disabled if threshold=NA.
decreasing: logical that indicates how the statistic/score should be ordered: TRUE orders by decreasing value (i.e. the greater the score the better), while FALSE orders by increasing value (i.e. the lower the score the better). The value of this argument also affects the way the filtering is performed (see argument threshold). Ordering is disabled if decreasing=NA.

Details

To see all available methods use markerScoreMethod().

Methods

extractMarkerssignature(object = "ExpressionSet"): The method extractMarkers for ExpressionSet objects calls extractMarkers on the expression matrix exprs(object).

Examples


# see available scoring methods
markerScoreMethod()

## [1] "Abbas"  "maxcol" "scorem" "HSD"

Extract Markers from Pure Samples.