Description Usage Arguments Value Examples
bc_seq_qc
evaluates sequences quality. See the return value for detail.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | 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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | 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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