per_base_quality: Compute the mean, median, and percentiles of quality score...

In qckitfastq: FASTQ Quality Control

Description

Compute the mean, median, and percentiles of quality score per base. This is returned as a data frame.

Usage

per_base_quality(infile, output_file = NA)

Arguments

infile	Path to a gzippped FASTQ file
output_file	File to write results in CSV format to. Default NA.

Value

A dataframe of the mean, median and quantiles of the FASTQ file

Author(s)

Wenyue Xing, [e-mail]

August Guang, [e-mail]

Examples

per_base_quality(system.file("extdata", "10^5_reads_test.fq.gz",
    package = "qckitfastq"))

Example output

    position q10 q25 median q75 q90
1          1  32  32     32  32  32
2          2  32  32     32  32  32
3          3  32  37     37  37  37
4          4  37  37     37  37  37
5          5  37  37     37  37  37
6          6  37  41     41  41  41
7          7  41  41     41  41  41
8          8  41  41     41  41  41
9          9  41  41     41  41  41
10        10  41  41     41  41  41
11        11  41  41     41  41  41
12        12  41  41     41  41  41
13        13  41  41     41  41  41
14        14  41  41     41  41  41
15        15  41  41     41  41  41
16        16  41  41     41  41  41
17        17  41  41     41  41  41
18        18  41  41     41  41  41
19        19  41  41     41  41  41
20        20  41  41     41  41  41
21        21  41  41     41  41  41
22        22  41  41     41  41  41
23        23  41  41     41  41  41
24        24  41  41     41  41  41
25        25  41  41     41  41  41
26        26  41  41     41  41  41
27        27  41  41     41  41  41
28        28  41  41     41  41  41
29        29  41  41     41  41  41
30        30  41  41     41  41  41
31        31  41  41     41  41  41
32        32  41  41     41  41  41
33        33  41  41     41  41  41
34        34  41  41     41  41  41
35        35  41  41     41  41  41
36        36  41  41     41  41  41
37        37  41  41     41  41  41
38        38  41  41     41  41  41
39        39  41  41     41  41  41
40        40  41  41     41  41  41
41        41  41  41     41  41  41
42        42  41  41     41  41  41
43        43  41  41     41  41  41
44        44  41  41     41  41  41
45        45  41  41     41  41  41
46        46  41  41     41  41  41
47        47  41  41     41  41  41
48        48  41  41     41  41  41
49        49  41  41     41  41  41
50        50  41  41     41  41  41
51        51  41  41     41  41  41
52        52  41  41     41  41  41
53        53  41  41     41  41  41
54        54  41  41     41  41  41
55        55  41  41     41  41  41
56        56  41  41     41  41  41
57        57  41  41     41  41  41
58        58  41  41     41  41  41
59        59  41  41     41  41  41
60        60  41  41     41  41  41
61        61  41  41     41  41  41
62        62  41  41     41  41  41
63        63  41  41     41  41  41
64        64  41  41     41  41  41
65        65  41  41     41  41  41
66        66  41  41     41  41  41
67        67  41  41     41  41  41
68        68  37  41     41  41  41
69        69  37  41     41  41  41
70        70  41  41     41  41  41
71        71  41  41     41  41  41
72        72  37  41     41  41  41
73        73  37  41     41  41  41
74        74  37  41     41  41  41
75        75  41  41     41  41  41
76        76  37  41     41  41  41
77        77  37  41     41  41  41
78        78  37  41     41  41  41
79        79  37  41     41  41  41
80        80  37  41     41  41  41
81        81  41  41     41  41  41
82        82  41  41     41  41  41
83        83  37  41     41  41  41
84        84  41  41     41  41  41
85        85  41  41     41  41  41
86        86  37  41     41  41  41
87        87  37  41     41  41  41
88        88  41  41     41  41  41
89        89  41  41     41  41  41
90        90  37  41     41  41  41
91        91  37  41     41  41  41
92        92  37  41     41  41  41
93        93  37  41     41  41  41
94        94  41  41     41  41  41
95        95  37  41     41  41  41
96        96  37  41     41  41  41
97        97  37  41     41  41  41
98        98  37  41     41  41  41
99        99  37  41     41  41  41
100      100  37  41     41  41  41

qckitfastq documentation built on Nov. 8, 2020, 5:24 p.m.