make_raw_nt | R Documentation |
Each sequence in the given vector becomes a column of the output matrix, with a row for each position. Shorter sequences are padded with a specific value at bottom of the matrix. With the defaults (see RAW_NT), A, C, G, and T (case insensitive) are encoded as 01, 02, 03, and 04, IUPAC codes are bitwise combinations of those values, padding values are 0x80, and any other character is 0x00.
make_raw_nt(seqs, map = RAW_NT, pad = 128, other = 0, chunksize = 8000)
seqs |
character vector of nucleotide sequences |
map |
raw vector with nucleotide names and byte values |
pad |
raw value to use for missing positions |
other |
raw value to use for nucleotides not in |
chunksize |
integer number of sequences to process at a time. For large (hundreds of thousands on up) numbers of input sequences this function can use a lot of memory, but limiting the number of sequences processed at once limits memory usage. |
raw matrix with positions on rows and sequences on columns
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