extractionMetrics: Get Extraction Metrics

In savR: Parse and analyze Illumina SAV files

Description

Extraction (intensity and FWHM) metrics for lane, tile, and cycle.

Usage

extractionMetrics(project)

## S4 method for signature 'savProject'
extractionMetrics(project)

Arguments

project

SAV project

Details

lane:

Lane number

tile:

Tile ID

cycle:

Cycle number

FWHM_[ACGT]:

Full width at half maximum for A, C, G, or T

int_[ACGT]:

Intensity of channel A, C, G, or T

datestamp:

Time/date stamp

Value

sorted data.frame of Extraction metrics

Examples

example(savR)
colnames(extractionMetrics(fc))

Example output

Loading required package: ggplot2

savR> fc <- savR(system.file("extdata", "MiSeq", package="savR"))

savR> fc
savProject instance with 1 lanes, 82 total cycles, and 2 sequence reads ( 1 sequencing and  1 indexed reads ).
 Default naming convention.
 With InterOp data for:  savCorrectedIntensityFormat (correctedIntensities)
  savQualityFormat (qualityMetrics)
  savTileFormat (tileMetrics)
  savExtractionFormat (extractionMetrics)
 
 [1] "lane"   "tile"   "cycle"  "FWHM_A" "FWHM_C" "FWHM_G" "FWHM_T" "int_A" 
 [9] "int_C"  "int_G"  "int_T" 

savR documentation built on Nov. 8, 2020, 7:03 p.m.