featureScores-methods: Methods to obtain scores for CMAPCollection gene sets from a...

Description Usage Arguments Value Methods Author(s) Examples

Description

These methods extract the scores for CMAPCollection gene set members from eSet or matrix objects and return them as a list (argument 'query') of lists (argument 'dat') with score vectors. Argument order determines the organization of the list, e.g. if 'query' is a CMAPCollection, one list element is returned for each gene set, containing all score vectors for the respective set. If 'simplify' is set to TRUE, score vectors are combined and a list of matrices is returned instead. Score vectors and matrices carries an additional 'sign' attribute corresponding to the sign annotated in the CMAPCollection.

Usage

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## S4 method for signature 'CMAPCollection,eSet'
featureScores(query, dat, element="z",simplify=TRUE)

## S4 method for signature 'CMAPCollection,matrix'
featureScores(query,dat, simplify=TRUE)

## S4 method for signature 'CMAPCollection,BigMatrix'
featureScores(query, dat, simplify=TRUE)

## S4 method for signature 'eSet,CMAPCollection'
featureScores(query, dat, element="z")

## S4 method for signature 'matrix,CMAPCollection'
featureScores(query, dat)

## S4 method for signature 'BigMatrix,CMAPCollection'
featureScores(query, dat)

## S4 method for signature 'CMAPCollection,numeric'
featureScores(query, dat)

## S4 method for signature 'CMAPCollection,CMAPCollection'
featureScores(query, dat)

## S4 method for signature 'numeric,CMAPCollection'
featureScores(query, dat)

## S4 method for signature 'CMAPCollection,matrix_or_big.matrix'
featureScores(query, dat, simplify = TRUE)

## S4 method for signature 'matrix_or_big.matrix,CMAPCollection'
featureScores(query, dat)

Arguments

query

A CMAPCollection, eSet or matrix.

dat

A CMAPCollection, eSet or matrix.

element

Character string specifying which assayDataElement to extract from eSet objects.

simplify

Logical: when possible, should score columns for each gene set collected in a matrix ?

Value

A nested list: one list element for each 'query', containing a list with score vectors for each 'dat'.

Methods

signature(query = "CMAPCollection", dat = "eSet")

}

signature(query = "CMAPCollection", dat = "matrix")

}

signature(query = "CMAPCollection", dat = "BigMatrix")

}

signature(query = "eSet", dat = "CMAPCollection")

}

signature(query = "matrix", dat = "CMAPCollection")

}

signature(query = "BigMatrix", dat = "CMAPCollection")

}

signature(query = "CMAPCollection", dat = "numeric")

}

signature(query = "CMAPCollection", dat = "CMAPCollection")

}

signature(query = "numeric", dat = "CMAPCollection")

}

signature(query = "matrix_or_big.matrix", dat = "CMAPCollection")

}

signature(query = "CMAPCollection", dat = "matrix_or_big.matrix")

}

Author(s)

Thomas Sandmann

Examples

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  data(gCMAPData)
  ## generate CMAPCollection with two sets (drug1, drug2)
  sets <- induceCMAPCollection(gCMAPData, "z", higher=-2, lower=2)[,1:2]
  sampleNames(sets) <- c("set1", "set2")
  
  ## extract per-gene scores as matrices
  res <- featureScores(sets, gCMAPData)
  class(res) ## list
  names(res) ## one element per set
  class(res[["set1"]]) ## matrix
  dim(res[["set1"]])

  ## or as lists of score vectors
  res2 <- featureScores(sets, gCMAPData, simplify=FALSE)
  class(res2[["set1"]]) ## list
  length(res2[["set1"]])

  ## stripplot for set2, colored by annotated sign
  m <- res[["set2"]][,"drug2"]
  colors <- ifelse( attr(res[["set2"]], "sign") == "up", "red", "blue")
  gene.sign <- factor( attr(res[["set2"]], "sign"))
  boxplot( 
    m ~ gene.sign,
    col=c("blue", "red"),
    ylab="z-score", 
    xlab="Query gene sign",
    main="Set 2"
    )

gCMAP documentation built on May 31, 2017, 2:35 p.m.

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