bc_seq_qc {CellBarcode} | R Documentation |
bc_seq_qc
evaluates sequences quality. See the return value for detail.
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)
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. |
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.
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)) ###