qc_problems: Inspect Problems in Aggregated FastQC Reports

Description Usage Arguments Value Functions Examples

View source: R/qc_problems.R

Description

Inspect problems in aggregated FastQC reports.

Usage

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qc_fails(object, element = c("sample", "module"), compact = TRUE)

qc_warns(object, element = c("sample", "module"), compact = TRUE)

qc_problems(object, element = c("sample", "module"), name = NULL,
  status = c("FAIL", "WARN"), compact = TRUE)

Arguments

object

an object of class qc_aggregate.

element

character vector specifying which element to check for inspecting problems. Allowed values are one of c("sample", "module"). Default is "sample".

  • If "sample", shows samples with more failed and/or warned modules

  • If "module", shows moduled that failed and/or warned in the most samples

compact

logical value. If TRUE, returns a compact output format; otherwise, returns a stretched format.

name

character vector containing the names of modules and/or samples of interest. See qc_read for valid module names. If name specified, a stretched output format is returned by default unless you explicitly indicate compact = TRUE.

status

character vector specifying the module status. Allowed values includes one or the combination of c("FAIL", "WARN"). If status = "FAIL", only modules with failed status are returned.

Value

Functions

Examples

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# Demo QC dir
qc.dir <- system.file("fastqc_results", package = "fastqcr")
qc.dir
# List of files in the directory
list.files(qc.dir)

# Aggregate the report
qc <- qc_aggregate(qc.dir, progressbar = FALSE)

# Display samples with failed modules
qc_fails(qc)
qc_fails(qc, compact = FALSE)

# Display samples with warned modules
qc_warns(qc)

# Module failed in the most samples
qc_fails(qc, "module")
qc_fails(qc, "module", compact = FALSE)

# Specify a module of interest
qc_problems(qc, "module",  name = "Per sequence GC content")

fastqcr documentation built on May 2, 2019, 2:13 a.m.