bc_seq_qc {CellBarcode}

R Documentation

Evaluates sequences quality

Description

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

Usage

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,

• top: a data.frame with top 50 most frequency sequence,

• distribution: a data.frame with the distribution of read depth. It contains nOccurrences (depth), and nReads (unique sequence) columns.

• base_quality_per_cycle: data.frame with base-pair location (NGS sequencing cycle) by row, and the base-pair quality summary by column, including Mean, P5 (5 P75 (75

• base_freq_per_cycle: data.frame with three columns: 1. Cycle, the sequence base-pair location (NGS sequencing cycle); 2. Base, DNA base; Count: reads count.

• summary: a numeric vector with following elements: total_read, median_read_length, p5_read_length, p95_read_length.

The barcodeQcSet is a list of barcodeQc.

Examples

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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