tileMetrics: Get Tile Metrics

In savR: Parse and analyze Illumina SAV files

Description

Returns the Tile Metrics SAV data.

Usage

tileMetrics(project)

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

Arguments

project

SAV project

Details

Metrics for each tile are encoded in the following format:

cluster density:	100
PF cluster density:	101
number of clusters:	102
number of PF clusters:	103
phasing for read N:	(200 + (N - 1) * 2)
prephasing for read N:	(201 + (N - 1) * 2)
percent aligned for read N:	(300 + N - 1)
control lane:	400

lane:

Lane number

tile:

Tile ID

code:

Code described above

value:

Value for code key

Value

sorted data.frame of tile metrics

References

Codes for Tile Metrics were obtained from the Python Illuminate package:
https://bitbucket.org/invitae/illuminate

Examples

example(savR)
colnames(tileMetrics(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"  "code"  "value"

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