basecontent {matchprobes} | R Documentation |
This function accepts a character vector representing the nucleotide sequences and computes the frequencies of each base (A, C, G, T).
basecontent(seq) countbases(seq, dna = TRUE)
seq |
Character vector. |
dna |
Logical value indicating whether the sequence is DNA
(TRUE ) or RNA (FALSE ) |
The base frequencies are calculated separately for
each element of x
.
The elements of x
can be in upper case, lower case
or mixed.
A matrix with 4 columns and length(x)
rows. The columns are
named A
, C
, T
, G
, and the values in each
column are the counts of the corresponding bases in the elements of
x
. When dna=FALSE
, the T
column is replaced with
a U
column.
R. Gentleman, W. Huber, S. Falcon
complementSeq
,reverseSeq
,
revcompDNA
, revcompRNA
v<-c("AAACT", "GGGTT", "ggAtT") basecontent(v) countbases(v)