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.
Expressed(
ExpressionSet,
cut.off,
method = "const",
comparison = "below",
n = NULL
)
a standard PhyloExpressionSet or DivergenceExpressionSet object.
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.
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"
.
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.
a numeric value for method = "n-set"
.
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.
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
#> [1] 449 9
# 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
#> [1] 830 9
# 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
#> [1] 830 9
# 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
#> [1] 24456 9
# 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
#> [1] 111 9