bc_seq_qc: Evaluates sequences quality

Description Usage Arguments Value Examples

Description

bc_seq_qc evaluates sequences quality. See the return value for detail.

Usage

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bc_seq_qc(x, sample_name = NULL)

bc_plot_seqQc(x)

## S4 method for signature 'ShortReadQ'
bc_seq_qc(x)

## S4 method for signature 'DNAStringSet'
bc_seq_qc(x)

## S4 method for signature 'data.frame'
bc_seq_qc(x)

## S4 method for signature 'integer'
bc_seq_qc(x)

## S4 method for signature 'character'
bc_seq_qc(x, sample_name = basename(x))

## S4 method for signature 'list'
bc_seq_qc(x, sample_name = names(x))

## S4 method for signature 'BarcodeQc'
bc_plot_seqQc(x)

## S4 method for signature 'BarcodeQcSet'
bc_plot_seqQc(x)

Arguments

x

A single or list of Fastq file, ShortReadQ object, DNAStringSet object, data.frame or named integer vector.

sample_name

A character vector with the length of sample number, used to set the sample name.

Value

A barcodeQc or a barcodeQcSet class. The barcodeQc is a list with four slots,

The barcodeQcSet is a list of barcodeQc.

Examples

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library(ShortRead)
# fastq file
fq_file <- system.file("extdata", "simple.fq", package="CellBarcode")
bc_seq_qc(fq_file)

# ShortReadQ
sr <- readFastq(fq_file[1])
bc_seq_qc(sr)

# DNAStringSet
ds <- sread(sr)
bc_seq_qc(ds)

# List of DNAStringSet
l <- list(sample1 = ds, sample2 = ds)
bc_plot_seqQc(bc_seq_qc(l))

# List of ShortRead
l_sr <- list(sample1 = sr, sample2 = sr)
bc_plot_seqQc(bc_seq_qc(l_sr))

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wenjie1991/CellBarocde documentation built on Dec. 23, 2021, 5:11 p.m.