◆ __init__()
| def cls.Int2Genes.CInt2Genes.__init__ |
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◆ IntervalOverlap()
| def cls.Int2Genes.CInt2Genes.IntervalOverlap |
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chrom, |
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Determine genes overlapping with an LD block.
@param chrom (@c String) Chromosome name.
@param begin Begin coordinate.
@param end End coordinate.
@return @c List of @ref cls.HSEnsgene.CHSEnsgenes or @c None of the
chromosome was not known.
◆ SNPandInterval()
| def cls.Int2Genes.CInt2Genes.SNPandInterval |
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chrom, |
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snpPos, |
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Relate (LD) interval with a SNP and get genes for this relationship.
We define an overlap as a non-zero intersection of the interval and
the gene. There is a multi level logic for finding the genes:
1. If the SNP location is contained in an interval, all (protein
coding) genes overlapping with this interval are reported,
indicated by a distance1=0. Furthermore, distance2=0 if the SNP is
in the gene. If the SNP is outside the gene, distance2 holds the
smaller distance to the gene begin or end. Only if there are no
genes overlapping with the query interval, the closest gene(s)
is/are determined, distance1=distance2=the smaller distance to the
gene's begin or end. (Remember, in the most extreme case two genes
can be exactly the same distance from a SNP!)
2. If the SNP is outside an LD block, the closest gene(s) is/are
output, again with a non-zero distance. These are then the same
genes as in the fallback of case 1.
@param chrom (@c String) Chromosome name.
@param snpPos Coordinate of SNP.
@param begin Begin coordinate.
@param end End coordinate.
@return @c None if the chromosome is unknown.
@c List of @c Tuple (distance1, distance2) as described above.
The documentation for this class was generated from the following file:
