Filters out rows from a matrix where the standard deviation is below (or above) a threshold. Also rows with less than two non-NA values are filtered as the standard deviation can not be computed. The filter can be used to, for example, remove rows from an expression matrix where the variation between samples is low.
Version | 1.1 |
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Bundle | tools |
Categories | Filter |
Specialties | generic |
Authors | Kristian Ovaska (kristian.ovaska@helsinki.fi) |
Issue tracker | View/Report issues |
Requires | R |
Source files | component.xml VariationFilter.r |
Usage | Example with default values |
Name | Type | Mandatory | Description |
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in | T (generic) | Mandatory | Input matrix. |
Name | Type | Description |
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out | T (generic) | Filtered matrix. |
Name | Type | Default | Description |
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columns | string | "*" | Names of columns that are included in standard deviation computation. However, all columns are always present in the output matrix. The special value * means all columns exept the first one having the rownames. |
filterSmallVariation | boolean | true | If true, rows with standard deviation BELOW the threshold are filtered out (normal operation). If false, rows with standard deviation ABOVE the threshold are filtered out. |
fraction | boolean | true | If true, the standard deviation threshold is a fraction of the mean of each row. Otherwise, the threshold is the nominal standard deviation. |
threshold | float | 0.1 | Standard deviation threshold as a percentage value of the mean of each row (if fraction=true) or as the absolute standard deviation (if fraction=false). For example, assume that fraction=true, the threshold is 0.1 and two rows have means 5 and 3; and standard deviations 0.2 and 0.4. The first row is removed since 0.2 is less than 0.1*5. The second row is kept since 0.4 is greater than 0.1*3. |
Test case | Parameters▼ | IN in |
OUT out |
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case1 | (missing) | in | out | |||
case2 | properties | in | out | |||
filterSmallVariation=false |
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case3 | properties | in | out | |||
columns=col1,col2,col3 |