read_samplesheet_: Load data from happyCompare samplesheets

In Illumina/happyCompare: Reporting toolbox for hap.py output

Description

Load hap.py results, build metrics and custom metadata into a happy_compare object using happyR.

Usage

read_samplesheet_(samplesheet, lazy = TRUE)

Arguments

samplesheet	A happyCompare samplesheet (data.frame). Required fields: Group.Id, Sample.Id, Replicate.Id, happy_prefix. Optional fields: build_metrics. Also supports additional metadata fields supplied as extra columns.
lazy	Do not load larger hap.py results until needed. Default: TRUE.

Value

A happy_compare object, with the following fields:

• samplesheet: the original samplesheet, stored as a data.frame.

• happy_results: a happy_result_list object that contains individual happy_result objects as defined in happyR.

• build_metrics: a build_metrics_list that contains a list of data.frames created from the csv files provided under the build_metrics column of the samplesheet.

• ids: a vector of unique identifiers for each result.

Examples

## Not run: 
happy_compare <- read_samplesheet(samplesheet_path = 'happyCompare_samplesheet.csv')

## End(Not run)

Illumina/happyCompare documentation built on July 12, 2019, 7:57 p.m.