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Ingy döt Net
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304
Task/P-value-correction/Go/p-value-correction.go
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304
Task/P-value-correction/Go/p-value-correction.go
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@ -0,0 +1,304 @@
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package main
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import (
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"fmt"
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"log"
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"math"
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"os"
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"sort"
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"strconv"
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"strings"
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)
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type pvalues = []float64
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type iv1 struct {
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index int
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value float64
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}
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type iv2 struct{ index, value int }
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type direction int
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const (
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up direction = iota
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down
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)
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// Test also for 'Unknown' correction type.
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var ctypes = []string{
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"Benjamini-Hochberg", "Benjamini-Yekutieli", "Bonferroni", "Hochberg",
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"Holm", "Hommel", "Šidák", "Unknown",
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}
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func minimum(p pvalues) float64 {
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m := p[0]
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for i := 1; i < len(p); i++ {
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if p[i] < m {
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m = p[i]
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}
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}
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return m
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}
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func maximum(p pvalues) float64 {
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m := p[0]
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for i := 1; i < len(p); i++ {
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if p[i] > m {
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m = p[i]
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}
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}
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return m
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}
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func adjusted(p pvalues, ctype string) (string, error) {
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err := check(p)
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if err != nil {
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return "", err
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}
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temp := pformat(adjust(p, ctype), 5)
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return fmt.Sprintf("\n%s\n%s", ctype, temp), nil
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}
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func pformat(p pvalues, cols int) string {
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var lines []string
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for i := 0; i < len(p); i += cols {
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fchunk := p[i : i+cols]
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schunk := make([]string, cols)
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for j := 0; j < cols; j++ {
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schunk[j] = strconv.FormatFloat(fchunk[j], 'f', 10, 64)
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}
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lines = append(lines, fmt.Sprintf("[%2d] %s", i, strings.Join(schunk, " ")))
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}
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return strings.Join(lines, "\n")
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}
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func check(p []float64) error {
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cond := len(p) > 0 && minimum(p) >= 0 && maximum(p) <= 1
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if !cond {
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return fmt.Errorf("p-values must be in range 0.0 to 1.0")
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}
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return nil
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}
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func ratchet(p pvalues, dir direction) {
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size := len(p)
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m := p[0]
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if dir == up {
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for i := 1; i < size; i++ {
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if p[i] > m {
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p[i] = m
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}
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m = p[i]
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}
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} else {
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for i := 1; i < size; i++ {
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if p[i] < m {
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p[i] = m
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}
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m = p[i]
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}
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}
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for i := 0; i < size; i++ {
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if p[i] > 1.0 {
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p[i] = 1.0
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}
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}
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}
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func schwartzian(p pvalues, mult pvalues, dir direction) pvalues {
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size := len(p)
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order := make([]int, size)
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iv1s := make([]iv1, size)
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for i := 0; i < size; i++ {
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iv1s[i] = iv1{i, p[i]}
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}
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if dir == up {
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sort.Slice(iv1s, func(i, j int) bool {
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return iv1s[i].value > iv1s[j].value
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})
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} else {
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sort.Slice(iv1s, func(i, j int) bool {
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return iv1s[i].value < iv1s[j].value
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})
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}
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for i := 0; i < size; i++ {
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order[i] = iv1s[i].index
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}
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pa := make(pvalues, size)
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for i := 0; i < size; i++ {
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pa[i] = mult[i] * p[order[i]]
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}
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ratchet(pa, dir)
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order2 := make([]int, size)
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iv2s := make([]iv2, size)
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for i := 0; i < size; i++ {
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iv2s[i] = iv2{i, order[i]}
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}
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sort.Slice(iv2s, func(i, j int) bool {
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return iv2s[i].value < iv2s[j].value
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})
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for i := 0; i < size; i++ {
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order2[i] = iv2s[i].index
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}
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pa2 := make(pvalues, size)
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for i := 0; i < size; i++ {
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pa2[i] = pa[order2[i]]
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}
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return pa2
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}
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func adjust(p pvalues, ctype string) pvalues {
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size := len(p)
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if size == 0 {
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return p
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}
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fsize := float64(size)
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switch ctype {
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case "Benjamini-Hochberg":
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mult := make(pvalues, size)
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for i := 0; i < size; i++ {
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mult[i] = fsize / float64(size-i)
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}
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return schwartzian(p, mult, up)
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case "Benjamini-Yekutieli":
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q := 0.0
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for i := 1; i <= size; i++ {
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q += 1.0 / float64(i)
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}
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mult := make(pvalues, size)
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for i := 0; i < size; i++ {
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mult[i] = q * fsize / (fsize - float64(i))
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}
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return schwartzian(p, mult, up)
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case "Bonferroni":
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p2 := make(pvalues, size)
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for i := 0; i < size; i++ {
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p2[i] = math.Min(p[i]*fsize, 1.0)
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}
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return p2
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case "Hochberg":
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mult := make(pvalues, size)
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for i := 0; i < size; i++ {
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mult[i] = float64(i) + 1
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}
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return schwartzian(p, mult, up)
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case "Holm":
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mult := make(pvalues, size)
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for i := 0; i < size; i++ {
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mult[i] = fsize - float64(i)
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}
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return schwartzian(p, mult, down)
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case "Hommel":
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order := make([]int, size)
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iv1s := make([]iv1, size)
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for i := 0; i < size; i++ {
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iv1s[i] = iv1{i, p[i]}
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}
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sort.Slice(iv1s, func(i, j int) bool {
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return iv1s[i].value < iv1s[j].value
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})
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for i := 0; i < size; i++ {
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order[i] = iv1s[i].index
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}
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s := make(pvalues, size)
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for i := 0; i < size; i++ {
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s[i] = p[order[i]]
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}
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m := make(pvalues, size)
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for i := 0; i < size; i++ {
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m[i] = s[i] * fsize / (float64(i) + 1)
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}
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min := minimum(m)
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q := make(pvalues, size)
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for i := 0; i < size; i++ {
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q[i] = min
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}
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pa := make(pvalues, size)
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for i := 0; i < size; i++ {
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pa[i] = min
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}
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for j := size - 1; j >= 2; j-- {
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lower := make([]int, size-j+1) // lower indices
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for i := 0; i < len(lower); i++ {
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lower[i] = i
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}
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upper := make([]int, j-1) // upper indices
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for i := 0; i < len(upper); i++ {
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upper[i] = size - j + 1 + i
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}
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qmin := float64(j) * s[upper[0]] / 2.0
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for i := 1; i < len(upper); i++ {
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temp := s[upper[i]] * float64(j) / (2.0 + float64(i))
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if temp < qmin {
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qmin = temp
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}
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}
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for i := 0; i < len(lower); i++ {
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q[lower[i]] = math.Min(s[lower[i]]*float64(j), qmin)
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}
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for i := 0; i < len(upper); i++ {
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q[upper[i]] = q[size-j]
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}
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for i := 0; i < size; i++ {
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if pa[i] < q[i] {
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pa[i] = q[i]
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}
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}
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}
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order2 := make([]int, size)
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iv2s := make([]iv2, size)
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for i := 0; i < size; i++ {
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iv2s[i] = iv2{i, order[i]}
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}
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sort.Slice(iv2s, func(i, j int) bool {
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return iv2s[i].value < iv2s[j].value
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})
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for i := 0; i < size; i++ {
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order2[i] = iv2s[i].index
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}
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pa2 := make(pvalues, size)
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for i := 0; i < size; i++ {
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pa2[i] = pa[order2[i]]
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}
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return pa2
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case "Šidák":
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p2 := make(pvalues, size)
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for i := 0; i < size; i++ {
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p2[i] = 1.0 - math.Pow(1.0-float64(p[i]), fsize)
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}
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return p2
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default:
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fmt.Printf("\nSorry, do not know how to do '%s' correction.\n", ctype)
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fmt.Println("Perhaps you want one of these?:")
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temp := make([]string, len(ctypes)-1)
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for i := 0; i < len(temp); i++ {
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temp[i] = fmt.Sprintf(" %s", ctypes[i])
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}
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fmt.Println(strings.Join(temp, "\n"))
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os.Exit(1)
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}
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return p
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}
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func main() {
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p := pvalues{
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4.533744e-01, 7.296024e-01, 9.936026e-02, 9.079658e-02, 1.801962e-01,
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8.752257e-01, 2.922222e-01, 9.115421e-01, 4.355806e-01, 5.324867e-01,
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4.926798e-01, 5.802978e-01, 3.485442e-01, 7.883130e-01, 2.729308e-01,
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8.502518e-01, 4.268138e-01, 6.442008e-01, 3.030266e-01, 5.001555e-02,
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3.194810e-01, 7.892933e-01, 9.991834e-01, 1.745691e-01, 9.037516e-01,
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1.198578e-01, 3.966083e-01, 1.403837e-02, 7.328671e-01, 6.793476e-02,
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4.040730e-03, 3.033349e-04, 1.125147e-02, 2.375072e-02, 5.818542e-04,
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3.075482e-04, 8.251272e-03, 1.356534e-03, 1.360696e-02, 3.764588e-04,
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1.801145e-05, 2.504456e-07, 3.310253e-02, 9.427839e-03, 8.791153e-04,
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2.177831e-04, 9.693054e-04, 6.610250e-05, 2.900813e-02, 5.735490e-03,
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}
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for _, ctype := range ctypes {
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s, err := adjusted(p, ctype)
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if err != nil {
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log.Fatal(err)
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}
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fmt.Println(s)
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}
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}
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