evidence

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v1.1.21 Latest Latest Go to latest Published: Apr 10, 2024 License: GPL-3.0 Imports: 15 Imported by: 0

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Repository

github.com/Ben-GO-package/acmg2015

Links

Open Source Insights

Documentation ¶

Index ¶

Variables
func CheckAFAllLowThen(item map[string]string, AFlist []string, threshold float64, includeEqual bool) bool
func CheckBA1(item map[string]string) string
func CheckBP1(item map[string]string) string
func CheckBP3(item map[string]string) string
func CheckBP4(item map[string]string) string
func CheckBP7(item map[string]string) string
func CheckBS1(item map[string]string) string
func CheckBS2(item map[string]string) string
func CheckDomain(item map[string]string) bool
func CheckOtherPathogenic(tbx *bix.Bix, item map[string]string, regions []Region) bool
func CheckPM1(item map[string]string, tbx *bix.Bix) string
func CheckPM2(item map[string]string) string
func CheckPM4(item map[string]string) string
func CheckPM5(item map[string]string) string
func CheckPP2(item map[string]string) string
func CheckPP3(item map[string]string, autoPVS1 bool) string
func CheckPS1(item map[string]string) string
func CheckPS4(item map[string]string) string
func CheckPVS1(item map[string]string, LOFList map[string]int, ...) string
func CompareBA1(item map[string]string, lostOnly bool)
func CompareBP1(item map[string]string, ClinVarBP1GeneList, HgmdBP1GeneList map[string]float64)
func CompareBP3(item map[string]string)
func CompareBP4(item map[string]string, lostOnly bool)
func CompareBP7(item map[string]string, lostOnly bool)
func CompareBS1(item map[string]string, lostOnly bool)
func CompareBS2(item map[string]string)
func ComparePM1(item map[string]string, tbx *bix.Bix)
func ComparePM2(item map[string]string)
func ComparePM4(item map[string]string)
func ComparePM5(item map[string]string, ...)
func ComparePP2(item map[string]string)
func ComparePP3(item map[string]string, lostOnly, autoPVS1 bool)
func ComparePS1(item map[string]string, ...)
func ComparePS4(item map[string]string)
func ComparePVS1(item map[string]string, LOFList map[string]int, ...)
func FindLOFIntoleranceGeneList(fileName, key string, pathogenicRegexp *regexp.Regexp) map[string]int
func FindPathogenicMissense(fileName, key string, pathogenicRegexp *regexp.Regexp) (map[string]int, map[string]int, map[string]int)
func LoadBA1(fileName string)
func LoadBP1(bp1geneList string)
func LoadBS2(fileName string)
func LoadPM1(pfamId, interproDomain string)
func LoadPP2(pp2geneList string)
func LoadPS1PM5(hgvs, pHgvs, aaPos string)
func PrintConflict(item map[string]string, rule, val string, keys ...string)
type Region

Constants ¶

This section is empty.

Variables ¶

View Source

var (
	BS2LateOnsetHomoThreshold = 5
	BS2NoLateOnsetThreshold   = 0
	BS2HitCountThreshold      = 2
)

View Source

var (
	PM2ARAFThreshold  = 0.005
	PM2ADAFThreshold  = 0.0
	PM2ADAFThreshold2 = 0.00001
)

View Source

var (
	PM1Function = regexp.MustCompile(`missense|cds-indel`)

	IsClinVarPLP = regexp.MustCompile(`Pathogenic|Likely_pathogenic`)
	IsHgmdDM     = regexp.MustCompile(`DM$|DM\|`)
)

View Source

var BA1AFList = []string{
	"ESP6500 AF",
	"1000G AF",
	"ExAC AF",
	"GnomAD AF",
	"ExAC EAS AF",
	"GnomAD EAS AF",
}

View Source

var BA1AFThreshold = 0.05

View Source

var BS1AFList = []string{
	"1000G AF",
	"ExAC AF",
	"GnomAD AF",
	"ESP6500 AF",
	"ExAC EAS AF",
	"GnomAD EAS AF",
}

View Source

var BS1MorbidityThreshold = 0.01

View Source

var BS2AF1List = []string{
	"GnomAD EAS AF",
	"GnomAD AF",
	"1000G AF",
	"ESP6500 AF",
	"ExAC EAS AF",
	"ExAC AF",
}

View Source

var BS2HomoList = []string{
	"ExAC HomoAlt Count",
	"GnomAD HomoAlt Count",
}

View Source

var FuncInfo = map[string]int{
	"splice-3":     3,
	"splice-5":     3,
	"init-loss":    3,
	"alt-start":    3,
	"frameshift":   3,
	"nonsense":     3,
	"stop-gain":    3,
	"span":         3,
	"missense":     2,
	"cds-del":      2,
	"cds-indel":    2,
	"cds-ins":      2,
	"splice-10":    2,
	"splice+10":    2,
	"coding-synon": 1,
	"splice-20":    1,
	"splice+20":    1,
}

Tier1 >1 LoF 3

View Source

var PM2AFList = []string{
	"ESP6500 AF",
	"1000G AF",
	"ExAC AF",
	"ExAC EAS AF",
	"GnomAD AF",
	"GnomAD EAS AF",
}

View Source

var PS4GWASdbORThreshold = 5.0

View Source

var PVS1AFThreshold = 0.05

View Source

var PVS1AFlist = []string{
	"GnomAD EAS AF",
	"GnomAD AF",
	"1000G AF",
	"ESP6500 AF",
	"ExAC EAS AF",
	"ExAC AF",
}

Functions ¶

func CheckAFAllLowThen ¶

func CheckAFAllLowThen(item map[string]string, AFlist []string, threshold float64, includeEqual bool) bool

func CheckBA1 ¶

func CheckBA1(item map[string]string) string

ture : "1" flase: "0"

func CheckBP1 ¶

func CheckBP1(item map[string]string) string

BP1

func CheckBP3 ¶

func CheckBP3(item map[string]string) string

ture : "1" flase: "0"

func CheckBP4 ¶

func CheckBP4(item map[string]string) string

ture : "1" flase: "0"

func CheckBP7 ¶

func CheckBP7(item map[string]string) string

ture : "1" flase: "0"

func CheckBS1 ¶

func CheckBS1(item map[string]string) string

ture : "1" flase: "0"

func CheckBS2 ¶

func CheckBS2(item map[string]string) string

func CheckDomain ¶

func CheckDomain(item map[string]string) bool

突变位点后有重要的蛋白结构功能区域

func CheckOtherPathogenic ¶

func CheckOtherPathogenic(tbx *bix.Bix, item map[string]string, regions []Region) bool

突变位点后有其他致病突变（基于公共数据库）位点

func CheckPM1 ¶

func CheckPM1(item map[string]string, tbx *bix.Bix) string

PM1

func CheckPM2 ¶

func CheckPM2(item map[string]string) string

PM2

func CheckPM4 ¶

func CheckPM4(item map[string]string) string

ture : "1" flase: "0" nil : ""

func CheckPM5 ¶

func CheckPM5(item map[string]string) string

PM5

func CheckPP2 ¶

func CheckPP2(item map[string]string) string

PP2

func CheckPP3 ¶

func CheckPP3(item map[string]string, autoPVS1 bool) string

ture : "1" flase: "0"

func CheckPS1 ¶

func CheckPS1(item map[string]string) string

PS1

func CheckPS4 ¶

func CheckPS4(item map[string]string) string

ture : "1" flase: "0" nil : ""

func CheckPVS1 ¶

func CheckPVS1(item map[string]string, LOFList map[string]int, transcriptInfo map[string][]Region, tbx *bix.Bix) string

func CompareBA1 ¶

func CompareBA1(item map[string]string, lostOnly bool)

func CompareBP1 ¶

func CompareBP1(item map[string]string, ClinVarBP1GeneList, HgmdBP1GeneList map[string]float64)

func CompareBP3 ¶

func CompareBP3(item map[string]string)

func CompareBP4 ¶

func CompareBP4(item map[string]string, lostOnly bool)

func CompareBP7 ¶

func CompareBP7(item map[string]string, lostOnly bool)

func CompareBS1 ¶

func CompareBS1(item map[string]string, lostOnly bool)

func CompareBS2 ¶

func CompareBS2(item map[string]string)

func ComparePM1 ¶

func ComparePM1(item map[string]string, tbx *bix.Bix)

func ComparePM2 ¶

func ComparePM2(item map[string]string)

func ComparePM4 ¶

func ComparePM4(item map[string]string)

func ComparePM5 ¶

func ComparePM5(item map[string]string, ClinVarPHGVSlist, ClinVarAAPosList, HGMDPHGVSlist, HGMDAAPosList map[string]int)

func ComparePP2 ¶

func ComparePP2(item map[string]string)

func ComparePP3 ¶

func ComparePP3(item map[string]string, lostOnly, autoPVS1 bool)

func ComparePS1 ¶

func ComparePS1(item map[string]string, ClinVarMissense, ClinVarPHGVSlist, HGMDMissense, HGMDPHGVSlist map[string]int)

func ComparePS4 ¶

func ComparePS4(item map[string]string)

func ComparePVS1 ¶

func ComparePVS1(item map[string]string, LOFList map[string]int, transcriptInfo map[string][]Region, tbx *bix.Bix)

func FindLOFIntoleranceGeneList ¶

func FindLOFIntoleranceGeneList(fileName, key string, pathogenicRegexp *regexp.Regexp) map[string]int

func FindPathogenicMissense ¶

func FindPathogenicMissense(fileName, key string, pathogenicRegexp *regexp.Regexp) (map[string]int, map[string]int, map[string]int)

func LoadBA1 ¶

func LoadBA1(fileName string)

func LoadBP1 ¶

func LoadBP1(bp1geneList string)

func LoadBS2 ¶

func LoadBS2(fileName string)

func LoadPM1 ¶

func LoadPM1(pfamId, interproDomain string)

func LoadPP2 ¶

func LoadPP2(pp2geneList string)

func LoadPS1PM5 ¶

func LoadPS1PM5(hgvs, pHgvs, aaPos string)

func PrintConflict ¶

func PrintConflict(item map[string]string, rule, val string, keys ...string)

Types ¶

type Region ¶

type Region struct {
	Seqid string
	//Source string
	Type       string
	Chromosome string
	Start      uint64
	End        uint64
	Strand     string
	Gene       string
}

Source Files ¶

View all Source files

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