ftrCOOL (version 2.0.0)

ANF_RNA: Accumulated riboNucleotide Frequency (ANF_RNA)

Description

This function replaces ribonucleotides with a four-length vector. The first three elements represent the ribonucleotides and the forth holds the frequency of the ribonucleotide from the beginning of the sequence until the position of the ribonucleotide in the sequence. 'A' will be replaced with c(1, 1, 1, freq), 'C' with c(0, 1, 0, freq),'G' with c(1, 0, 0, freq), and 'U' with c(0, 0, 1, freq).

Usage

ANF_RNA(seqs, outFormat = "mat", outputFileDist = "", label = c())

Arguments

seqs

is a FASTA file containing ribonucleotide sequences. The sequences start with '>'. Also, seqs could be a string vector. Each element of the vector is a ribonucleotide sequence.

outFormat

(output format) can take two values: 'mat'(matrix) and 'txt'. The default value is 'mat'.

outputFileDist

shows the path and name of the 'txt' output file.

label

is an optional parameter. It is a vector whose length is equivalent to the number of sequences. It shows the class of each entry (i.e., sequence).

Value

The output depends on the outFormat parameter which can be either 'mat' or 'txt'. If outFormat is 'mat', the function returns a feature matrix for sequences with the same length such that the number of columns is (sequence length)*(4) and the number of rows is equal to the number of sequences. If the outFormat is 'txt', the output is written to a tab-delimited file.

References

Chen, W., Tran, H., Liang, Z. et al. Identification and analysis of the N6-methyladenosine in the Saccharomyces cerevisiae transcriptome. Sci Rep 5, 13859 (2015).

Examples

# NOT RUN {
fileLNC<-system.file("extdata/Carica_papaya101RNA.txt",package="ftrCOOL")
mat<-ANF_RNA(seqs = fileLNC,outFormat="mat")

# }