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QuantileFilter

Filters values from numeric matrices that are below or above quantile limits. Filtered values are set to NA or, if removeMissing is true, rows with all missing values are removed from the output. Quantile limits are between 0 and 1. For example, lowQuantile=0.05 and highQuantile=0.95 would set to NA all values that are below 5'th percentile or above 95'th percentile. By default filtering is done for each column independently (see parameter colsIndependently).

There can be one or two input matrices. If there are two matrices, they must have identical dimensions. A value is filtered if it is outside quantile limits in both matrices.

Version 1.0
Bundle tools
Categories Filter
Specialties generic
Authors Kristian Ovaska (kristian.ovaska@helsinki.fi)
Issue tracker View/Report issues
Requires R
Source files component.xml QuantileFilter.r
Usage Example with default values

Type parameters (generics)

Inputs

Name Type Mandatory Description
in1 T1 (generic) Mandatory Input matrix 1.
in2 T2 (generic) Optional Input matrix 2.

Outputs

Name Type Description
out1 T1 (generic) Output matrix 1 where filtered cells have been replaced with NA, or possibly removed if removeMissing is true.
out2 T2 (generic) Output matrix 2 where filtered cells have been replaced with NA, or possibly removed if removeMissing is true.

Parameters

Name Type Default Description
colsIndependently boolean true If true, filtering is done for each column independently. If false, filtering is done based on all columns in a matrix: a row is set to NA values if all the values are above highQuantile limit or all the values are below lowQuantile limit.
highQuantile float 1 High threshold, between 0 and 1 inclusive. Set to 1 to disable high threshold filtering.
lowQuantile float 0 Low threshold, between 0 and 1 inclusive. Set to 0 to disable low threshold filtering.
removeMissing boolean true If true, do not include rows that have only missing values in the output. If false, include the rows but print NA's for all columns.

Test cases

Test case Parameters IN
in1
IN
in2
OUT
out1
OUT
out2
case1_LL properties in1 in2 out1 out2

lowQuantile=0.51,
removeMissing=false

case2_LH properties in1 in2 out1 out2

lowQuantile=0.51,
highQuantile=0.74,
removeMissing=false

case3_one properties in1 (missing) out1 out2

lowQuantile=0.26,
highQuantile=0.74

case4_by_row properties in1 in2 out1 out2

lowQuantile=0.51,
highQuantile=0.74,
removeMissing=false,
colsIndependently=false


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