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FoldIndexR addition

Package changes implementing the FoldIndexR() equation into idpr and the idprofiles.

WilliamMc authored on 11/03/2022 07:31:29
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@@ -46,6 +46,7 @@ Kyte, J., & Doolittle, R. F. (1982). A simple method for
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 Other scaled hydropathy functions: 
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 \code{\link{KDNorm}},
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+\code{\link{foldIndexR}()},
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 \code{\link{scaledHydropathyGlobal}()},
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 \code{\link{scaledHydropathyLocal}()}
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 }
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Updating sequenceCheck

WilliamMc authored on 26/08/2020 22:50:34
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@@ -7,8 +7,8 @@
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 meanScaledHydropathy(sequence, roundScore = NA)
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 }
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 \arguments{
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-\item{sequence}{amino acid sequence as a single character string
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-or vector of single characters.
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+\item{sequence}{amino acid sequence as a single character string,
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+a vector of single characters, or an AAString object.
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 It also supports a single character string that specifies
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 the path to a .fasta or .fa file.}
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Proofreading Documentation

WilliamMc authored on 16/07/2020 22:26:29
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@@ -30,7 +30,7 @@ aaVector <- c("A", "C", "D", "E", "F",
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               "G", "H", "I", "K", "L",
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               "M", "N", "P", "Q", "R",
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               "S", "T", "V", "W", "Y")
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- #Alternativly, .fasta files can also be used by providing
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+ #Alternatively, .fasta files can also be used by providing
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 #Calculate the mean scaled hydropathy
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  meanScaledHydropathy(aaString)
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Vignette and Documentation Updates

Proofreading and updating documentation for the package

WilliamMc authored on 17/06/2020 18:50:56
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@@ -10,7 +10,7 @@ meanScaledHydropathy(sequence, roundScore = NA)
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 \item{sequence}{amino acid sequence as a single character string
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 or vector of single characters.
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 It also supports a single character string that specifies
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-the locaion of a .fasta or .fa file.}
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+the path to a .fasta or .fa file.}
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 \item{roundScore}{Number of decimals the score will be rounded to.
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 NA by default.}
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@@ -19,7 +19,7 @@ NA by default.}
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 A numeric value equal to the Mean Scaled Hydropathy.
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 }
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 \description{
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-This funciton utlilizes the scaledHydropathyGlobal() function and
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+This function utilizes the scaledHydropathyGlobal() function and
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   easily returns the averaged hydropathy as a numeric value.
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 }
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 \examples{
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Added example documentation and combined similar scripts into the same file

WilliamMc authored on 05/06/2020 22:41:26
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@@ -1,5 +1,5 @@
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 % Generated by roxygen2: do not edit by hand
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-% Please edit documentation in R/meanScaledHydropathy.R
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+% Please edit documentation in R/scaledHydropathy.R
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 \name{meanScaledHydropathy}
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 \alias{meanScaledHydropathy}
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 \title{Calculate the Mean Scaled Hydropathy}
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@@ -22,6 +22,20 @@ A numeric value equal to the Mean Scaled Hydropathy.
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 This funciton utlilizes the scaledHydropathyGlobal() function and
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   easily returns the averaged hydropathy as a numeric value.
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 }
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+\examples{
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+#Amino acid sequences can be character strings
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+aaString <- "ACDEFGHIKLMNPQRSTVWY"
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+#Amino acid sequences can also be character vectors
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+aaVector <- c("A", "C", "D", "E", "F",
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+              "G", "H", "I", "K", "L",
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+              "M", "N", "P", "Q", "R",
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+              "S", "T", "V", "W", "Y")
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+ #Alternativly, .fasta files can also be used by providing
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+
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+#Calculate the mean scaled hydropathy
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+ meanScaledHydropathy(aaString)
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+ meanScaledHydropathy(aaVector)
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+}
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 \references{
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 Kyte, J., & Doolittle, R. F. (1982). A simple method for
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   displaying the hydropathic character of a protein.
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Initial commit

WilliamMc authored on 13/05/2020 00:45:34
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new file mode 100644
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@@ -0,0 +1,38 @@
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/meanScaledHydropathy.R
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+\name{meanScaledHydropathy}
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+\alias{meanScaledHydropathy}
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+\title{Calculate the Mean Scaled Hydropathy}
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+\usage{
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+meanScaledHydropathy(sequence, roundScore = NA)
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+}
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+\arguments{
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+\item{sequence}{amino acid sequence as a single character string
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+or vector of single characters.
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+It also supports a single character string that specifies
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+the locaion of a .fasta or .fa file.}
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+
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+\item{roundScore}{Number of decimals the score will be rounded to.
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+NA by default.}
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+}
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+\value{
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+A numeric value equal to the Mean Scaled Hydropathy.
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+}
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+\description{
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+This funciton utlilizes the scaledHydropathyGlobal() function and
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+  easily returns the averaged hydropathy as a numeric value.
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+}
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+\references{
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+Kyte, J., & Doolittle, R. F. (1982). A simple method for
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+  displaying the hydropathic character of a protein.
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+  Journal of molecular biology, 157(1), 105-132.
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+}
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+\seealso{
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+\code{\link{KDNorm}} for residue values.
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+
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+Other scaled hydropathy functions: 
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+\code{\link{KDNorm}},
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+\code{\link{scaledHydropathyGlobal}()},
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+\code{\link{scaledHydropathyLocal}()}
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+}
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+\concept{scaled hydropathy functions}