inst/report_input_file.md

In philliplab/MotifBinner: Bin reads by Motif

Input File

Sys.time()

## [1] "2015-03-19 13:08:56 SAST"

A summary of the input sequences

print(seq_dat)

##   A DNAStringSet instance of length 14575
##         width seq
##     [1]   352 TATGGGATCAAAGTCTAAAACCATGTGTA...TGCTTACCTAACTGAGCGTGTGGCAAGGC
##     [2]   352 TATGGGACGAAAGCCTCAAGCCATGTGTA...TGTTAGATGTTCTGAGCGTGTGGCAAGGC
##     [3]   361 TATGGGACGAAAGTCTAAAGCCATGTGTA...TGTATTGGGGCCTGAGCGTGTGGCAAGGC
##     [4]   419 AATGTCAGCACAGTACAATGTACACATGG...ACTCATGCAACCTGAGCGTGTGGCAAGGC
##     [5]   351 TATGGGACCAAAGTCTAAAGCCATGTGTA...GTGCTATCGAACTGAGCGTGTGGCAAGGC
##     ...   ... ...
## [14571]   352 TATGGGACGAAAGTCTAAAGCCATGTGTA...TGGTACACAAGCTGAGCGTGTGGCAAGGC
## [14572]   352 TATGGGACGAAAGCCTCAAGCTATGTGTA...TGCATTTAAAACTGAGCGTGTGGCAAGGC
## [14573]   352 TATGGGACGAAAGTCTCAAACCATGTGTA...TGGCTCAAGTACTGAGCGTGTGGCAAGGC
## [14574]   361 TATGGGATCAAAGTCTAAAACCATGTGTA...TGAATCCTCTACTGAGCGTGTGGCAAGGC
## [14575]   352 TATGGGACGAAAGTCTAAAGCCATGTGTA...TGTAATTGCGACCGAGCGTGTGGCAAGGC

The letter frequencies

Counts of the letters in the input sequences.

x <- apply(consensusMatrix(seq_dat), 1, sum)
x <- x[x != 0]
kable(data.frame(letter = names(x),
                 count = x,
                 count_per_seq = round(x/length(seq_dat),2),
                 row.names = 1:length(x)))

|letter | count| count_per_seq| |:------|-------:|-------------:| |A | 1889682| 129.65| |C | 1028655| 70.58| |G | 973999| 66.83| |T | 1394116| 95.65| |N | 12| 0.00|

Normalized counts of the letters in the input sequences.

x_freq <- round(x/sum(x), 4)
kable(data.frame(letter = names(x_freq),
                 count = x_freq,
                 row.names = 1:length(x_freq)))

|letter | count| |:------|------:| |A | 0.3575| |C | 0.1946| |G | 0.1842| |T | 0.2637| |N | 0.0000|

barplot(x/sum(x),
        main = 'Normalized counts of the letters\nin the input sequences')

The sequence lengths

hist(width(seq_dat),
     main = "Histogram of the lengths of the input sequences",
     xlab = "Sequence Length",
     ylab = "Number of Sequences")

philliplab/MotifBinner documentation built on Sept. 2, 2020, 11:41 a.m.