Filter for Expressed Genes

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Description

This function takes an ExpressionSet object and removes genes from the gene expression matrix that have an expression level below, above, or below AND above a defined cut.off value. Hence, this function allows to remove genes that have been defined as not expressed or outliers and returns an ExpressionSet retaining only expressed genes.

Usage

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Expressed(ExpressionSet, cut.off, method = "const", comparison = "below",
  n = NULL)

Arguments

ExpressionSet

a standard PhyloExpressionSet or DivergenceExpressionSet object.

cut.off

a numeric value specifying the expression cut-off to define genes as not expressed (comparison = "below") , outliers (comparison = "above"), or both (comparison = "both"). See comparison for details. In case comparison = "both", the cut.off argument must be a two dimensional vector defining the lower cut.off value at the first position and the upper cut.off value at the second position.

method

a method defining how to treat gene expression values in multiple stages. The corresponding method that is chosen allows to control the stage-wise fulfillment of the threshold criteria. Options are "const", "min-set", and "n-set".

comparison

a character string specifying whether genes having expression levels below, above, or below AND above (both) the cut.off value should be excluded from the dataset. In case comparison = "both" is chosen, the cut.off argument must be a two dimensional vector defining the lower cut.off value at the first position and the upper cut.off value at the second position.

n

a numeric value for method = "n-set".

Details

This filter function allows users to remove genes from the ExpressionSet object that undercut or exceed a certain expression level cut.off.

Following extraction criteria are implemented in this function:

  • const: all genes that have at least one stage that undercuts or exceeds the expression cut.off will be excluded from the ExpressionSet. Hence, for a 7 stage ExpressionSet genes passing the expression level cut.off in 6 stages will be retained in the ExpressionSet.

  • min-set: genes passing the expression level cut.off in ceiling(n/2) stages will be retained in the ExpressionSet, where n is the number of stages in the ExpressionSet.

  • n-set: genes passing the expression level cut.off in n stages will be retained in the ExpressionSet. Here, the argument n needs to be specified.

Author(s)

Hajk-Georg Drost

Examples

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data(PhyloExpressionSetExample)

# remove genes that have an expression level below 8000 
# in at least one developmental stage
FilterConst <- Expressed(ExpressionSet = PhyloExpressionSetExample, 
                         cut.off       = 8000, 
                         method        = "const",
                         comparison    = "below")
                              
dim(FilterConst) # check number of retained genes

# remove genes that have an expression level below 8000 
# in at least 3 developmental stages 
# (in this case: ceiling(7/2) = 4 stages fulfilling the cut-off criteria)
FilterMinSet <- Expressed(ExpressionSet = PhyloExpressionSetExample, 
                          cut.off       = 8000, 
                          method        = "min-set",
                          comparison    = "below")
                               
dim(FilterMinSet) # check number of retained genes

# remove genes that have an expression level below 8000 
# in at least 5 developmental stages (in this case: n = 2 stages fulfilling the criteria)
FilterNSet <- Expressed(ExpressionSet = PhyloExpressionSetExample, 
                        cut.off       = 8000, 
                        method        = "n-set",
                        comparison    = "below",
                        n             = 2)
                               
dim(FilterMinSet) # check number of retained genes



# remove expression levels that exceed the cut.off criteria
FilterMinSet <- Expressed(ExpressionSet = PhyloExpressionSetExample, 
                          cut.off       = 12000, 
                          method        = "min-set",
                          comparison    = "above")
                               
dim(FilterMinSet) # check number of retained genes


# remove expression levels that undercut AND exceed the cut.off criteria
FilterMinSet <- Expressed(ExpressionSet = PhyloExpressionSetExample, 
                          cut.off       = c(8000,12000), 
                          method        = "min-set",
                          comparison    = "both")
                               
dim(FilterMinSet) # check number of retained genes

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