calcGC: Calculate GC percent

In HELP: Tools for HELP data analysis

Description

Function to calculate GC percent from a nucleotide sequence input

Usage

calcGC(x, ...)

Arguments

x	characters containing nucleotide sequence (ex: "ATCGGAA") or an object of class ExpressionSet
...	Other arguments passed to methods: allow vector of characters specifying what other characters to allow in sequence (default is "N")

Value

Returns a numerical value (from 0 to 1) indicating the C+G content of the sequence, corresponding to the fraction of (C+G)/(A+T+C+G...). A value of NA is returned if the function encounters an error that prevents proper calculation of GC percent.

Author(s)

Reid F. Thompson ([e-mail])

See Also

calcGC-methods, calcTm

Examples

#demo(pipeline,package="HELP")

calcGC("AAAACGCG")
calcGC(sequence="cXgXcXgXcXgX",allow="X")

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

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HELP documentation built on Nov. 8, 2020, 11:08 p.m.