|
Sleipnir
|
Dab2Dad combines multiple DAT/DAB files, possibly including a gold standard answer file in addition to multiple datasets, into a DAD file as described by Sleipnir::CDatasetCompact.
Dab2Dad -o <data.dad> <data.dab>*
Create an output dataset DAD file data.dad consisting of the gene pairs and values from all DAT/DAB files data.dab, which must be accompanied by corresponding QUANT files.
Dab2Dad -o <data.dad> -n <network.xdsl> -a <answers.dab> <data.dab>*
Create an output dataset DAD file data.dad appropriate for use in training or evaluating Bayesian networks with the structure network.xdsl, using the gold standard answers in answers.dab and the data in the DAT/DAB files data.dab.
Dab2Dad -i <data.dad>
Output (to standard output) the contents of data.dad as a tab-delimited text table.
Dab2Dad -i <data.dad> -m -l <gene1> -L <gene2>
Open data.dad using memory mapping and output all values stored for the gene pair gene1 and gene2.
package "Dab2Dad"
version "1.0"
purpose "Single/multiple data file interconversion"
defgroup "Input-Output"
groupoption "input" i "Input DAD file"
string typestr="filename" group="Input-Output"
groupoption "load" a "Persistent load DAD file"
string typestr="filename" group="Input-Output"
groupoption "network" n "Input Bayesian network (X)DSL"
string typestr="filename" group="Input-Output"
section "Main"
option "output" o "Output DAD file"
string typestr="filename"
option "answers" w "Answer DAT/DAB file"
string typestr="filename"
option "directory" d "Directory with DAB files"
string typestr="directory" default="."
section "Miscellaneous"
option "everything" e "Include pairs without answers"
flag off
option "continuous" c "Output continuous values"
flag off
section "Learning/Evaluation"
option "genes" g "Gene inclusion file"
string typestr="filename"
option "genex" G "Gene exclusion file"
string typestr="filename"
section "Lookups"
option "lookup1" l "First lookup gene"
string
option "lookup2" L "Second lookup gene"
string
option "lookups" t "Lookup gene set"
string typestr="filename"
option "lookupp" T "Lookup pair set"
string typestr="filename"
option "quantize" q "Discretize lookups"
flag off
option "paircount" P "Only count pairs above cutoff"
int default="-1"
section "Optional"
option "mask" k "Mask DAT/DAB file"
string typestr="filename"
option "memmap" m "Memory map input/output"
flag off
option "verbosity" v "Message verbosity"
int default="5"
| Flag | Default | Type | Description |
|---|---|---|---|
| None | None | DAT/DAB files | Input DAT/DAB files to be combined into a DAD. |
| -i | None | DAD file | If given, load this binary DAD file and save it as text to standard output or to -o. |
| -a | None | DAD file | If given, load this binary DAD file and retain a shared memory map (can theoretically be used to force a DAD into virtual memory for rapid access by other processes). |
| -n | None | (X)DSL file | If given, combine DAT/DABs from -w and -d into a DAD file appropriate for use with the given Bayes net. Discretization and node order information will be read from the given network. |
| -o | stdout | DAD file | If given, output DAD is written as binary to the requested file. |
| -w | None | DAT/DAB file | Must be given with -n; indicates an answer file DAT/DAB to be included in the DAD along with datasets from the command line. |
| -d | None | Directory | Must be given with -n; indicates the directory in which DAT/DAB files corresponding to the input network's node IDs will be found. |
| -e | off | Flag | If on, output DAD will include data for all gene pairs; if off, it will only contain data for gene pairs with a value present in the answer file. |
| -g | None | Text gene list | If given, use only gene pairs for which both genes are in the list. For details, see Sleipnir::CDat::FilterGenes. |
| -G | None | Text gene list | If given, use only gene pairs for which neither gene is in the list. For details, see Sleipnir::CDat::FilterGenes. |
| -l | None | String | If given, lookup all values for pairs involving the requested gene. |
| -L | None | String | If given with -l, lookup all values for the requested gene pair. |
| -t | None | Gene text file | If given with -l, lookup all pairs between -l and the given gene set. If given alone, lookup all pairs between genes in the given set. |
| -T | None | Gene pair text file | Tab-delimited text file containing one pair of gene IDs per row. If given, lookup values for all requested pairs. |
| -q | off | Flag | If on, quantize data from input DAT/DABs before outputting lookup results. |
| -k | None | DAT/DAB file | If given, process only gene pairs present in the given DAT/DAB with a score greater than zero. |
| -m | off | Flag | If given, memory map the input files when possible. DAT and PCL inputs cannot be memmapped. |
1.7.6.1