QCplot: QC plot by read position

In aliafdz/QApckg: Quality assessment for Miseq data derived from viral sequencing

QC plot by read position

Description

Draws a scatter plot with Phred score values by read position.

Usage

QCplot(fvnm1, fvnm2, snm, SW = FALSE, FL = FALSE)

Arguments

fvnm1, fvnm2	Matrix or array containing Phred score values by read position for 0.05, 0.25, 0.5, 0.75 and 0.95 quantiles. If a QC by position plot for R1 and R2 files is required, both arguments are needed, one for each file.
snm	Character indicating the name of the pool of evaluated reads. Only required when both fvnm1 and fvnm2 are provided.
SW	Logical indicating if the plot should include quality profile by SW (Sliding Window). If TRUE, Phred Scores are computed as moving averages for windows of 10 base length slid along the sequence.
FL	Logical indicating if the first argument corresponds to the scores of FLASH extended reads. If TRUE, only fvnm1 argument is required.

Details

fvnm1 and fvnm2 arguments are obtanied from the QCscores function with argument byPos=TRUE.

Value

A scatter plot with desired values will be shown in the active plots window.

Note

This function is only defined for correct execution of PoolQCbyPos function from the same package.

Author(s)

Alicia Aranda

See Also

PoolQCbyPos, QCscores

Examples

flashDir <- "./flash"
flashfiles <- list.files(flashDir,recursive=TRUE,full.names=TRUE,include.dirs=TRUE)
lst1 <- QCscores(file.path(flashDir,flashfiles[1]),byPos=T)
fvnm1 <- lst1$fvnq
QCplot(fvnm1,FL=TRUE) # QC plot for FLASH fastq file
QCplot(fvnm1,SW=TRUE,FL=TRUE) # QC plot by SW for FLASH fastq file

aliafdz/QApckg documentation built on June 2, 2022, 10:29 a.m.