readstats: Read tRNA Gene Count Statistics

In fredysiegrist/statanacoseq: Statistical Analyses of Codon Usage in Custom Genome Sequences

Description

readstats read-in anticodon count from tRNAscan-2.0 or similar summary files from GtRNAdb2 homepage

Usage

readstats(fileno = 156, chunksize = 1)

Arguments

fileno	Index number of html-file in the working directory
chunksize	The maximum number of lines of data to be read

Details

Puts gene count into a table according to anticodon sequence on tRNA. This functions works but on the summary files there are some not nicely behaving statistics where the new filtering methods have not been applied as for the fasta files.

Value

tRNA gene count Table

Author(s)

Siegrist, F. and Cannarozzi, G. M. [e-mail]

See Also

seqinr statanacoseq http://gtrnadb.ucsc.edu/GtRNAdb2/

Examples

setwd("E:/R/viruses")
filecount <- length(dir(pattern=".stats.html$"))
vir_optcodon <- as.list(rep(data.frame(x=0), times=filecount))
for (n in 1:filecount) vir_optcodon[[n]] <- readstats(n)
names(vir_optcodon) <- sapply(dir(pattern="stats.html$"), function(x) strsplit(x, "-")[[1]][1])

fredysiegrist/statanacoseq documentation built on May 16, 2019, 2:44 p.m.