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Jb linreg #67

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merged 5 commits into from
Nov 4, 2015
Merged

Jb linreg #67

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ab76b2a
added :Double to help IntelliJ with breeze type inference (killing th…
jbloom22 Nov 4, 2015
6e43727
modified String to Option[String] here.
jbloom22 Nov 4, 2015
7ae9345
added filter to famOf, sexOf, and phenoOf to fix Kyle's bug
jbloom22 Nov 4, 2015
be9dcee
removed option.get, replaced with flatMap
jbloom22 Nov 4, 2015
ccf224f
removed all option.get, replaced with flatMap
jbloom22 Nov 4, 2015
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8 changes: 4 additions & 4 deletions src/main/scala/org/broadinstitute/hail/methods/LinearRegression.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -143,11 +143,11 @@ object LinearRegression {

val qtx = qtBc.value * x
val qty = qtyBc.value
val xxp = xx - (qtx dot qtx)
val xyp = xy - (qtx dot qty)
val yyp = yypBc.value
val xxp: Double = xx - (qtx dot qtx)
val xyp: Double = xy - (qtx dot qty)
val yyp: Double = yypBc.value

val b = xyp / xxp
val b: Double = xyp / xxp
val se = math.sqrt((yyp / xxp - b * b) / d)
val t = b / se
val p = 2 * tDistBc.value.cumulativeProbability(-math.abs(t))
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11 changes: 5 additions & 6 deletions src/main/scala/org/broadinstitute/hail/methods/Pedigree.scala
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Expand Up @@ -74,14 +74,13 @@ case class Pedigree(trioMap: Map[Int, Trio]) {
.toMap
.groupByKey

def dadOf: Map[Int, Int] = completeTrios.map(t => (t.kid, t.dad.get)).toMap
def momOf: Map[Int, Int] = completeTrios.map(t => (t.kid, t.mom.get)).toMap
def sexOf: Map[Int, Sex] = completeTrios.map(t => (t.kid, t.sex.get)).toMap
def famOf: Map[Int, String] = trios.map(t => (t.kid, t.fam.get)).toMap
def phenoOf: Map[Int, Phenotype] = trios.map(t => (t.kid, t.pheno.get)).toMap
def dadOf: Map[Int, Int] = completeTrios.flatMap(t => t.dad.map(d => (t.kid, d))).toMap
def momOf: Map[Int, Int] = completeTrios.flatMap(t => t.mom.map(m => (t.kid, m))).toMap
def sexOf: Map[Int, Sex] = trios.flatMap(t => t.sex.map(s => (t.kid, s))).toMap
def famOf: Map[Int, String] = trios.flatMap(t => t.fam.map(f => (t.kid, f))).toMap
def phenoOf: Map[Int, Phenotype] = trios.flatMap(t => t.pheno.map(p => (t.kid, p))).toMap

def sexDefinedForAll: Boolean = trios.forall(_.sex.isDefined)

def phenoDefinedForAll: Boolean = trios.forall(_.pheno.isDefined)

def nSatisfying(filters: (Trio => Boolean)*): Int = trios.count(t => filters.forall(_(t)) )
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