Readme.md

In jframi/snpclust: shiny app to visualize and manually correct clustering of fluorescence based SNP markers.

Version 1.1 (20/06/2024)

Installation

Install remotes package if not already done

install.packages(remotes)

Install snpclust package

remotes::install_github("jframi/snpclust")

Then load snpclust

library(snpclust)

Usage

After installing the package, the shiny app can be run using:

runmanclust()

Load data from file

Choose an input file that contain fluorescence values and calls for one or several SNPs and one or several DNA plates. Adjust the file format parameters to read the input file. Format parameters are OK when the first rows of your files appear correctly. Match the columns of your file to the column names that the app is expecting, then click OK. Then select a SNP and possibly a Plate to display a scatter plot of fluorescence values. You can switch to Show New Call view, select individual genotypes in the plot using the lasso tool, and score selected points.

Use BrAPI

BrAPI can be used at two different levels in the app: - To retrieve sample metadata when genotyping data are loaded from a file in which samples are identified with sampleDbIds that can be found at a BrAPI endpoint - To retrieve genotyping data from a BrAPI endpoint that implements Genotyping section of BrAPI

To use BrAPI, it is required to define BrAPI endpoints before running the application.

options(brapi.cons=list(GIGWA_SOUTHGREEN=brapirv2::brapi_connect(secure = TRUE,
                                                                 protocol = "https://",
                                                                 db = "gigwa.southgreen.fr",
                                                                 port = 80,
                                                                 apipath = "gigwa/rest",
                                                                 multicrop = FALSE,
                                                                 granttype = "token",
                                                                 clientid = "brapir",
                                                                 bms = FALSE),
                        My_BMS_Server=brapirv2::brapi_connect(db="mybms.bmspro.io",
                                                              port=80,
                                                              bms=F,
                                                              secure = TRUE,
                                                              protocol = "https://",
                                                              apipath = "bmsapi",
                                                              granttype = "token",
                                                              multicrop = TRUE,
                                                              commoncropname = "mycrop")))

Retrieve samples information

One a file with genotyping data has been loaded, sample metadata can be retrieved from a BMS BrAPI endpoint. Select the BMS connection endpoint, provide a token and click on Connect Select the BMS program and click on "Fetch samples information". Then click on Update samples information and use the Sample_Plot_Label and Sample column in the Match columns step.

Load data from BrAPI

To load genotyping data directly from a BrAPI endpoint, select "From BrAPI" in the Load data tab. Select the BrAPI endpoint, provide a token and click on Connect. Then select a Program and a Study and proceed directly to the Clustering Tab.

Launch snpclust with BrAPI connection settings passed through the url

snpclust can be invoked with BrAPI connection seetings passed as URL parameters. URL parameters are: - mainapiURL: the is the url of the BrAPI endpoint - mainbrapiprogram: BrAPI programDbId - mainbrapistudy: BrAPI studyDbId - maintoken: authorized token to access data

jframi/snpclust documentation built on June 28, 2024, 10:30 a.m.