README.md

In vivizhou/MDfilter: Mendelian disease variant filtering

MDfilter

Title: Mendelian disease variant filtering

Version: 0.0.0.1 Author: Wei Zhou

The package provides a few functions for family-based genetic variant filtering to identify pathogenic variant for Mendelian diseases.

Install the package:

devtools::install_github("vivizhou/MDfilter")
library(MDfilter)
?importTXT
?cleanData
?filterVariant
?plotPedigree

Example usage:

Import txt file from ANNOVAR annotation on vcf files

```{r, results='hide'} file.path <- "data.vcf.full_annotation.txt" rawData <- importTXT(file.path)

#### Import pedigree file

```{r, results='hide'}
pedigreePlot <- readxl::read_excel("pedigree.xlsx", na = "NA", sheet = 1)
head(pedigreePlot)

Get included IDs (match the variant data file), affected IDs, and unaffected IDs. Also specify female and male IDs if X-linked recessive is assumed.

```{r, results='hide'} familyIDs <- pedigreePlot$id includedSubjectIDs <- familyIDs[familyIDs %in% colnames(rawData)] affectedIDs <- pedigreePlot[(pedigreePlot$affected == 1) & !is.na(pedigreePlot$affected), "id", drop = TRUE] paste0("Affected IDs: ", affectedIDs) unaffectedIDs <- pedigreePlot[pedigreePlot$affected == 0 & !is.na(pedigreePlot$affected == 0), "id", drop = TRUE] paste0("Unaffected IDs: ", unaffectedIDs)

#### Clean imported data file

```{r, results='hide'}
cleanedData <- cleanData(rawData, includeIDs = includedSubjectIDs,
                              removeMultiallelicSites = FALSE,
                              remove.nocall.pct = 0.2,
                              QD.threshold = 5,
                              saveRData = FALSE, savePath = "DataExample/",
                              label = "testCleanedData")

Filter the variants

```{r, results='hide'} filteredVariants <- filterVariant(data.name = cleanedData, affected.id = affectedIDs, unaffected.id = unaffectedIDs, inheritance.pattern = "AD", femaleIDs = NULL, maleIDs = NULL, gene.name = NULL, frequency.col = c("ExAC_All", "X1000G_ALL", "ExAC_NFE", "X1000G_EUR"), freq.threshold = 0.005, protein.altering = TRUE, include.UTRs = FALSE, include.synonymous = FALSE, include.nonframeshift = FALSE, CADD.threshold = 15, save.path = "DataExample/", save.txt = TRUE, label = "test", save.genelist = TRUE)

#### Plot pedigree file for APC gene

```{r, results='markup'}
plotPedigree(variant.list = filteredVariants,
              pedigree.data = pedigreePlot,
              includeIDs = includedSubjectIDs,
              gene.name = "APC",
              save.path = "DataExample",
              savePNG = TRUE,
              label = "testPlot")

vivizhou/MDfilter documentation built on May 21, 2022, 2:15 a.m.