qualityMetrics: Get Quality Metrics data

In savR: Parse and analyze Illumina SAV files

Description

Quality metric by lane, tile and cycle.

Usage

qualityMetrics(project)

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

Arguments

project

SAV project

Details

lane:

Lane number

tile:

Tile ID

cycle:

Cycle number

Q1-Q50:

Number of clusters with quality of indicated column

Value

sorted data.frame of quality data

Examples

example(savR)
colnames(qualityMetrics(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" "Q1"    "Q2"    "Q3"    "Q4"    "Q5"    "Q6"   
[10] "Q7"    "Q8"    "Q9"    "Q10"   "Q11"   "Q12"   "Q13"   "Q14"   "Q15"  
[19] "Q16"   "Q17"   "Q18"   "Q19"   "Q20"   "Q21"   "Q22"   "Q23"   "Q24"  
[28] "Q25"   "Q26"   "Q27"   "Q28"   "Q29"   "Q30"   "Q31"   "Q32"   "Q33"  
[37] "Q34"   "Q35"   "Q36"   "Q37"   "Q38"   "Q39"   "Q40"   "Q41"   "Q42"  
[46] "Q43"   "Q44"   "Q45"   "Q46"   "Q47"   "Q48"   "Q49"   "Q50"  

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