Description Usage Arguments Details Value Author(s) References Examples
Returns a dataframe with the desired score (e.g. Zscore) for observation
based on the algorithm for calculating Z scores described in Lu et al 2008.
Calculations are done based on value of parameter
.
1 | mad.scores(data, parameter='FLATCODE', n=3, out=c('Zscore', 'label'), ...)
|
data |
Dataframe or Matrix of inputs for which the zscore is to be calculated |
parameter |
The parameter (given by column name) on which the mad score is to be calculated. This is the only non-numeric column allowed. |
n |
the number of Median Absolute Deviations (MAD) from the center which is considered a 'mutant' or putative hit. |
out |
The desired output value, either the 'Zscore' (quantitative) or 'label' (qualitative, 3 classes). |
... |
Other parameters. |
Data should be presorted according to any identifiers and parameter
as labels not used in the calculations will be removed. data
should
be a dataframe with parameter
as a factor (or character) and the
rest of the values numeric.
Each column (other than parameter
) is considered independent. Rows
(individual responses) are extracted from data
according to
parameter
and the MAD is calculated for each column (assay).
If out = 'label', then a test is done to see if the result (Zscore) is
greater or less than abs(n
) and scored 'high' or 'low' accordingly.
mad.scores
returns a dataframe containing the Zscores or labels for
the observations. The first column will contain the parameter
label.
If data will be returned in the same order as it was input so long as a sort
based on parameter
was completed ahead of time.
Shannon M. Bell
Bell SM, Burgoon LD, Last RL. MIPHENO: Data normalization for high throughput metabolite analysis. BMC Bioinformatics 2012, 13(10)
Lu Y, et al. New connections across pathways and cellular processes: Industrialized mutant screening reveals novel associations between diverse phenotypes in Arabidopsis. Plant Physiol 2010, 152(2):529-540
1 | #See the sweave document in the corresponding paper for examples
|
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