/// <summary>
/// Loads a map.
/// </summary>
/// <returns>The map.</returns>
/// <param name="mapFileName">Map file name.</param>
/// <param name="configData">Config data.</param>
/// <param name="maxRange">Max range.</param>
public static TssRegulatoryMap LoadMap(
string mapFileName,
List <int> promoterRange,
int maxRange,
double confidenceThreshold)
{
var mapProperties = new MapLinkFilter
{
PromoterUpstreamRange = promoterRange[0],
PromoterDownstreamRange = promoterRange.Count == 1 ? promoterRange[0] : promoterRange[1],
MaximumLinkLength = maxRange,
ConfidenceThreshold = confidenceThreshold,
};
return(TssRegulatoryMap.LoadMap(mapFileName, mapProperties));
}
public void FilterMap(MapLinkFilter.LinkType linkType)
{
var mapLinkFilter = new MapLinkFilter
{
LinkTypeFilter = linkType,
};
var map = TssRegulatoryMap.LoadMap(this.MapFileName, mapLinkFilter);
var outputMapFile = this.MapFileName.Replace(".bed", "." + linkType.ToString() + ".bed");
var tssSet = this.GeneMap ?
this.ExpressionFiles.First().Value.Genes :
this.ExpressionFiles.First().Value.Transcripts;
WriteMap(map, tssSet, this.HistoneName, outputMapFile);
}
/// <summary>
/// Convert the map to genes.
/// </summary>
public void Convert()
{
MapLinkFilter filter = new MapLinkFilter
{
MaximumLinkLength = this.MaxRange,
ConfidenceThreshold = this.PvalueThreshold,
LinkTypeFilter = MapLinkFilter.LinkType.Any,
};
TssRegulatoryMap map = TssRegulatoryMap.LoadMap(this.MapFileName, filter);
var expression = new GtfExpressionFile(
GtfExpressionFile.ExpressionTypeFromString(this.RnaSource),
this.AnnotationFileName);
var geneMap = map.ConvertToGenes(IUnknown.QueryInterface <IExpressionData>(expression));
foreach (var link in geneMap.Links)
{
var geneLocation = expression.Transcripts[link.TranscriptName];
string[] lineData = new string[]
{
geneLocation.Chromosome,
geneLocation.Start.ToString(),
geneLocation.End.ToString(),
link.GeneName,
"NA",
geneLocation.Strand,
link.LocusName,
link.Correlation.ToString(),
link.ConfidenceScore.ToString(),
link.LinkLength.ToString(),
this.HistoneName,
link.TranscriptName,
};
Console.WriteLine(string.Join("\t", lineData));
}
}
/// <summary>
/// Execute this instance.
/// </summary>
public void Execute()
{
var filter = new MapLinkFilter {
};
if (this.Threshold >= 0)
{
filter.ConfidenceThreshold = this.Threshold;
}
var corrMap = TssRegulatoryMap.LoadMap(this.MapFileName, filter);
if (corrMap.Count == 0)
{
return;
}
if (this.UseGenes)
{
corrMap = corrMap.ConvertToGenes();
}
var scores = corrMap.Links.OrderBy(x => x.ConfidenceScore).ToArray();
const int thresholdCount = 10;
double binSize = (double)scores.Length / thresholdCount;
var binEdges = new double[] { 0.0 }
.Concat(Enumerable.Range(1, 9).Select(x => scores[(int)Math.Floor(x * binSize)].ConfidenceScore))
.Concat(new double[] { 1 })
.Reverse()
.ToArray();
var binColors = new string[] { "192,192,192" }
.Concat(binEdges
.Select((x, i) => string.Format(
"{0},0,{1}",
(int)((double)i / (thresholdCount - 1) * 255),
255 - (int)((double)i / (thresholdCount - 1) * 255))))
.ToList();
var links = corrMap.Links.Select(x =>
{
var upstreamLocation = x.LocusLocation.Start < x.TssLocation.DirectionalStart ? x.LocusLocation : x.TssLocation;
var downstreamLocation = x.LocusLocation.End > x.TssLocation.DirectionalStart ? x.LocusLocation : x.TssLocation;
int upstreamLength = x.LocusLocation.Start < x.TssLocation.DirectionalStart ? x.LocusSize : 1;
int downstreamLength = x.LocusLocation.End > x.TssLocation.DirectionalStart ? x.LocusSize : 1;
int regionStart = upstreamLocation.Start - (upstreamLength == 1 ? 1 : 0);
int regionEnd = downstreamLocation.End + (downstreamLength == 1 ? 1 : 0);
var blockCount = "2";
var blockSizes = upstreamLength + "," + downstreamLength;
var blockStarts = x.LinkLength > 0 ?
"0," + (regionEnd - regionStart - 1) :
"0," + (regionEnd - regionStart - x.LocusSize);
if (x.LocusLocation.OverlapsDirectionalStart(x.TssLocation))
{
blockCount = "1";
blockStarts = "0";
blockSizes = x.LocusSize.ToString();
}
return(new string[]
{
x.LocusLocation.Chromosome,
regionStart.ToString(),
regionEnd.ToString(),
x.LocusLocation.Name + "_" + x.TssLocation.Name,
x.ConfidenceScore.ToString(),
upstreamLocation == x.LocusLocation ? "+" : "-",
regionStart.ToString(),
regionEnd.ToString(),
binColors[Bin(x.ConfidenceScore, binEdges)],
blockCount,
blockSizes,
blockStarts
});
})
.ToList();
Tables.ToNamedTsvFile(
this.OutputFile,
links,
new string[] { "track name=regulatory_map description=\"Regulatory Map\" itemRgb=\"On\"" });
}
