library(Biostrings) options(scipen=999) em_dat <- report_dat$em_dat attach(em_dat)
Sys.time()
print(prefix) print(suffix) print(motif_length)
n_matched <- length(motif_dat$matched_seq) n_unmatched <- length(motif_dat$unmatched_seq) n_total <- n_matched + n_unmatched kable(data.frame(seq_matched_count = n_matched, seq_matched_perc = 100*round(n_matched / n_total, 4), seq_unmatched_count = n_unmatched, seq_unmatched_perc = 100*round(n_unmatched / n_total, 4)))
print(motif_dat$matched_seq)
Counts of the letters in the matched sequences.
x <- apply(consensusMatrix(motif_dat$matched_seq), 1, sum) x <- x[x != 0] kable(data.frame(letter = names(x), count = x, count_per_seq = round(x/length(motif_dat$matched_seq),2), row.names = 1:length(x)))
Normalized counts of the letters in the matched sequences.
x_freq <- round(x/sum(x), 4) kable(data.frame(letter = names(x_freq), count = x_freq, row.names = 1:length(x_freq)))
barplot(x/sum(x), main = 'Normalized counts of the letters\nin the matched sequences')
hist(width(motif_dat$matched_seq), main = "Histogram of the lengths of the matched sequences", xlab = "Sequence Length", ylab = "Number of Sequences")
print(motif_dat$unmatched_seq)
Counts of the letters in the unmatched sequences.
x <- apply(consensusMatrix(motif_dat$unmatched_seq), 1, sum) x <- x[x != 0] kable(data.frame(letter = names(x), count = x, count_per_seq = round(x/length(motif_dat$unmatched_seq),2), row.names = 1:length(x)))
Normalized counts of the letters in the unmatched sequences.
x_freq <- round(x/sum(x), 4) kable(data.frame(letter = names(x_freq), count = x_freq, row.names = 1:length(x_freq)))
barplot(x/sum(x), main = 'Normalized counts of the letters\nin the unmatched sequences')
hist(width(motif_dat$unmatched_seq), main = "Histogram of the lengths of the unmatched sequences", xlab = "Sequence Length", ylab = "Number of Sequences")
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