//private static IEnumerable<InputRow> CreateRowListQuery(List<KeyValuePair<string, string>> cidGroupAndInputFileNameList, string pTargetHeader, List<string> keyNameList)
//{
// foreach (var cidGroupAndInputFileName in cidGroupAndInputFileNameList)
// {
// string cidGroup = cidGroupAndInputFileName.Key;
// string inputFileName = cidGroupAndInputFileName.Value;
// Console.WriteLine("Reading file " + inputFileName);
// MBT.Escience.CounterWithMessages counterWithMessages = new MBT.Escience.CounterWithMessages("reading cidGroup " + cidGroup + " file, line #{0}", 10000, null);
// string header;
// foreach (var line in SpecialFunctions.TabFileTable(inputFileName, includeWholeLine:false, out header))
// {
// counterWithMessages.Increment();
// List<string> keyList = keyNameList.Select(keyName => line[keyName]).ToList();
// InputRow inputRow = new InputRow
// {
// //SplitIndex = int.Parse(line.GetValueOrDefault("splitIndex", "0")),
// Cid = line["cid"],
// CidGroup = cidGroup,
// TargetVal = int.Parse(line["TargetVal"]),
// PTarget = double.Parse(line[pTargetHeader]),
// KeyList = keyList
// };
// yield return inputRow;
// }
// }
//}
private static IEnumerable <InputRow> CreateRowListQuery(Predicate <int> splitIndexFilter, KeyValuePair <string, string> cidGroupAndInputFileName, string pTargetHeader, List <string> keyNameList)
{
string header1 = "pathway cid nullIndex pTarget targetVal logLikelihood splitIndex splitCount workIndex workCount testCidIndex testCidCount";
string header2 = "pathway cid nullIndex pTarget(or prediction) targetVal logLikelihood(or score) splitIndex splitCount workIndex workCount testCidIndex testCidCount";
string[] fields = header1.Split('\t');
Dictionary <string, int> fieldToIndex = fields.Select((key, index) => new KeyValuePair <string, int>(key, index)).
ToDictionary(keyAndIndex => keyAndIndex.Key, keyAndIndex => keyAndIndex.Value);
List <int> keyIndexList = keyNameList.Select(keyName => fieldToIndex[keyName]).ToList();
int cidIndex = fieldToIndex["cid"];
int targetValIndex = fieldToIndex["targetVal"];
int pTargetHeaderIndex = fieldToIndex[pTargetHeader];
int splitIndexIndex = fieldToIndex["splitIndex"];
string cidGroup = cidGroupAndInputFileName.Key;
string inputFileName = cidGroupAndInputFileName.Value;
Console.WriteLine("Reading file " + inputFileName);
MBT.Escience.CounterWithMessages counterWithMessages = new MBT.Escience.CounterWithMessages("reading cidGroup " + cidGroup + " file, line #{0}", 100000, null);
using (TextReader textReader = File.OpenText(inputFileName))
{
//pathway cid nullIndex pTarget targetVal logLikelihood splitIndex splitCount workIndex workCount testCidIndex testCidCount
// 0 1 2 3 4
string line;
while (null != (line = textReader.ReadLine()))
{
if (line == header1 || line == header2)
{
continue; //not break;
}
counterWithMessages.Increment();
string[] valueList = line.Split('\t');
List <string> keyList = keyIndexList.Select(keyIndex => valueList[keyIndex]).ToList();
if (!splitIndexFilter(int.Parse(valueList[splitIndexIndex])))
{
continue; // not break;
}
InputRow inputRow = new InputRow
{
//SplitIndex = int.Parse(line.GetValueOrDefault("splitIndex", "0")),
Cid = valueList[cidIndex],
CidGroup = cidGroup,
TargetVal = int.Parse(valueList[targetValIndex]),
PTarget = double.Parse(valueList[pTargetHeaderIndex]),
KeyList = keyList
};
yield return(inputRow);
}
}
}
private static ResultsRow CreateResultRow(KeyValuePair <string, List <InputRow> > keyListAsStringAndRowList, MBT.Escience.CounterWithMessages counterWithMessages, ParallelOptions parallelOptions)
{
counterWithMessages.Increment();
string keyListAsString = keyListAsStringAndRowList.Key;
List <InputRow> rowListAll = keyListAsStringAndRowList.Value;
var cidGroupAndRowListList =
(from row in rowListAll
group row by row.CidGroup into g
select new KeyValuePair <string, List <InputRow> >(g.Key, g.ToList())
).ToList();
//Creates a result for each cidGroup
var cidGroupToPValue =
(
from cidGroupAndRowList in cidGroupAndRowListList
let cidGroup = cidGroupAndRowList.Key
let rowList = cidGroupAndRowList.Value
orderby cidGroup
select new { cidGroup, Z0AndPValue = ComputeZ0AndPValue(rowList, row => row.PTarget, row => row.TargetVal, parallelOptions) }
).ToDictionary(pair => pair.cidGroup, pair => pair.Z0AndPValue);
double z0OfAll = cidGroupToPValue.Values.Select(z0AndPValue => z0AndPValue.Key).Sum() / Math.Sqrt(cidGroupToPValue.Count);
double pOfAll = 1.0 - SpecialFunctions.ZScoreToOneTailedPValue(z0OfAll, 1e-10);
//Create the group for all
ResultsRow result = new ResultsRow {
KeyListAsString = keyListAsString, CidGroupToZ0AndPValue = cidGroupToPValue, ComboPValue = pOfAll
};
return(result);
}