Takes the output of a minc modelling function and computes False Discovery Rate thresholds.
mincFDR(buffer, ...) # S3 method for mincSingleDim mincFDR(buffer, df, mask = NULL, method = "qvalue", ...) # S3 method for mincLogLikRatio mincFDR(buffer, mask = NULL, ...) # S3 method for mincLmer mincFDR(buffer, mask = NULL, method = "fdr", ...) # S3 method for mincMultiDim mincFDR(buffer, columns = NULL, mask = NULL, df = NULL, method = "FDR", statType = NULL, ...)
| buffer | The results of a mincLm type run. |
|---|---|
| ... | extra parameters to pass to methods |
| df | The degrees of freedom - normally this can be determined from the input object. |
| mask | Either a filename or a numeric vector representing a mask only values inside the mask will be used to compute the threshold. |
| method | The method used to compute the false discovery rate. Options are "FDR" and "pFDR". |
| columns | A vector of column names. By default the threshold will be computed for all columns; with this argument the computation can be limited to a subset. |
| statType | This should be either a "t","F","u","chisq" or "tlmer" depending upon the type of statistic being thresholded. |
A object of type mincQvals with the same number of columns
as the input (or the subset specified by the columns argument to
mincFDR). Each column now contains the qvalues for each voxel. Areas
outside the mask (if a mask was specified) will be represented by a
value of 1. The result also has an attribute called "thresholds"
which contains the 1, 5, 10, 15, and 20 percent false discovery rate
thresholds.
This function uses the qvalue package to compute the
False Discovery Rate threshold for the results of a mincLm
computation. The False Discovery Rate represents the percentage of
results expected to be a false positive. Two implementations can be
used as specified by the method argument. "FDR" uses the
implementation in p.adjust, whereas "pFDR" is a version of the
postivie False Discovery Rate as found in John Storey's qvalue
package. The main interface functions are
mincFDR.mincMultiDim The workhorse function, used to compute q-values and thresholds for sets of minc volumes
mincFDR.logLikRatio Similar to above, but calculates thresholds by parametric bootstrap when possible
mincFDR.mincSingleDim Used when mincLm-like results are written out and read back in
either to the same or another R session. In this case it loses it's minMultiDim class
and must be converted back
vertexFDR Used with results of a vertexLm-like command. Results are converted internally to resemble a mincMultiDim and processed as normal
mincSingleDim: mincSingleDim
mincLogLikRatio: mincLogLikRatio
mincLmer: mincLmer
mincMultiDim: mincMultiDim
mincWriteVolume,mincLm,mincWilcoxon or mincTtest
# NOT RUN { getRMINCTestData() # read the text file describing the dataset gf <- read.csv("/tmp/rminctestdata/test_data_set.csv") # run a linear model relating the data in all voxels to Genotype vs <- mincLm(jacobians_fixed_2 ~ Sex, gf) # compute the False Discovery Rate qvals <- mincFDR(vs) # }