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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
Showing1 changed files
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@@ -87,6 +87,7 @@ Kyte, J., & Doolittle, R. F. (1982). A simple method for
87 87
 
88 88
 Other scaled hydropathy functions: 
89 89
 \code{\link{KDNorm}},
90
+\code{\link{foldIndexR}()},
90 91
 \code{\link{meanScaledHydropathy}()},
91 92
 \code{\link{scaledHydropathyLocal}()}
92 93
 }
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Updating sequenceCheck

WilliamMc authored on 26/08/2020 22:50:34
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@@ -7,8 +7,8 @@
7 7
 scaledHydropathyGlobal(sequence, plotResults = FALSE, proteinName = NA, ...)
8 8
 }
9 9
 \arguments{
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-\item{sequence}{amino acid sequence as a single character string
11
-or vector of single characters.
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+\item{sequence}{amino acid sequence as a single character string,
11
+a vector of single characters, or an AAString object.
12 12
 It also supports a single character string that specifies
13 13
 the path to a .fasta or .fa file.}
14 14
 
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Proofreading Documentation

WilliamMc authored on 16/07/2020 22:26:29
Showing1 changed files
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@@ -34,6 +34,17 @@ This is used to calculate the scaled hydropathy of an amino acid
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   The output is either a data frame or graph
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   showing the matched scores for each residue along the sequence.
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 }
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+\section{Plot Colors}{
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+
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+  For users who wish to keep a common aesthetic, the following colors are
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+  used when plotResults = TRUE. \cr
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+  \itemize{
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+  \item Dynamic line colors: \itemize{
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+  \item Close to 0 = "skyblue3" or "#6CA6CD"
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+  \item Close to 1 = "chocolate1" or "#FF7F24"
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+  \item Close to midpoint = "grey65" or "#A6A6A6"}}
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+}
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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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@@ -42,7 +53,7 @@ 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
46 57
 ##The path to the file as a character string
47 58
 
48 59
 exampleDF <- scaledHydropathyGlobal(aaString,
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fixing notes by bioccheck

WilliamMc authored on 07/07/2020 20:51:57
Showing1 changed files
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@@ -40,8 +40,8 @@ aaString <- "ACDEFGHIKLMNPQRSTVWY"
40 40
 #Amino acid sequences can also be character vectors
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 aaVector <- c("A", "C", "D", "E", "F",
42 42
               "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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+              "M", "N", "P", "Q", "R",
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+              "S", "T", "V", "W", "Y")
45 45
 #Alternativly, .fasta files can also be used by providing
46 46
 ##The path to the file as a character string
47 47
 
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Updating based on BiocCheck

WilliamMc authored on 07/07/2020 16:12:39
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@@ -4,8 +4,6 @@
4 4
 \alias{scaledHydropathyGlobal}
5 5
 \title{Protein Scaled Hydropathy Calculations}
6 6
 \usage{
7
-scaledHydropathyGlobal(sequence, plotResults = FALSE, proteinName = NA, ...)
8
-
9 7
 scaledHydropathyGlobal(sequence, plotResults = FALSE, proteinName = NA, ...)
10 8
 }
11 9
 \arguments{
... ...
@@ -24,12 +22,6 @@ optional setting to include the name in the plot title.}
24 22
 \item{...}{any additional parameters, especially those for plotting.}
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 }
26 24
 \value{
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-if \code{plotResults = TRUE}, a graphical representation data.
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-  Average is shown by the horizontal line.
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-  If \code{plotResults = FALSE}, a dataframe is reported
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-  with each amino acid and each residue value shown.
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-  Score for each residue shown in the column "Hydropathy".
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-
33 25
 if \code{plotResults = TRUE}, a graphical representation data.
34 26
   Average is shown by the horizontal line.
35 27
   If \code{plotResults = FALSE}, a data frame is reported
... ...
@@ -37,11 +29,6 @@ if \code{plotResults = TRUE}, a graphical representation data.
37 29
   Score for each residue shown in the column "Hydropathy".
38 30
 }
39 31
 \description{
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-This is used to calculate the scaled hydropathy of an amino acid
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-  sequence for each residue in the sequence.
42
-  The output is either a dataframe or graph
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-  showing the matched scores for each residue along the sequence.
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-
45 32
 This is used to calculate the scaled hydropathy of an amino acid
46 33
   sequence for each residue in the sequence.
47 34
   The output is either a data frame or graph
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@@ -67,57 +54,19 @@ exampleDF <- scaledHydropathyGlobal(aaVector,
67 54
 head(exampleDF)
68 55
 
69 56
 #plotResults = TRUE will output a ggplot
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-\dontrun{
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-  scaledHydropathyGlobal(aaString,
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-                         plot = T)
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-
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-  #since it is a ggplot, you can change or annotate the plot
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-  gg <- scaledHydropathyGlobal(aaVector,
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-                               plot = T)
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-  gg <- gg + ggplot2::ylab("Local Hydropathy")
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-  gg <- gg + ggplot2::geom_text(data = exampleDF,
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-                                ggplot2::aes(label = AA,
80
-                                             y = Hydropathy + 0.1))
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-  plot(gg)
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-}
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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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-##The path to the file as a character string
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-
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-exampleDF <- scaledHydropathyGlobal(aaString,
94
-                                    plotResults = FALSE)
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-head(exampleDF)
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-
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-exampleDF <- scaledHydropathyGlobal(aaVector,
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-                                    plotResults = FALSE)
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-head(exampleDF)
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-
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-#plotResults = TRUE will output a ggplot
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-\dontrun{
103 57
   scaledHydropathyGlobal(aaString,
104
-                         plot = T)
58
+                         plotResults = TRUE)
105 59
 
106 60
   #since it is a ggplot, you can change or annotate the plot
107 61
   gg <- scaledHydropathyGlobal(aaVector,
108
-                               plot = T)
62
+                               plotResults = TRUE)
109 63
   gg <- gg + ggplot2::ylab("Local Hydropathy")
110 64
   gg <- gg + ggplot2::geom_text(data = exampleDF,
111 65
                                 ggplot2::aes(label = AA,
112 66
                                              y = Hydropathy + 0.1))
113 67
   plot(gg)
114 68
 }
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-}
116 69
 \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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-
121 70
 Kyte, J., & Doolittle, R. F. (1982). A simple method for
122 71
   displaying the hydropathic character of a protein.
123 72
   Journal of molecular biology, 157(1), 105-132.
... ...
@@ -125,13 +74,6 @@ Kyte, J., & Doolittle, R. F. (1982). A simple method for
125 74
 \seealso{
126 75
 \code{\link{KDNorm}} for residue values.
127 76
 
128
-\code{\link{KDNorm}} for residue values.
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-
130
-Other scaled hydropathy functions: 
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-\code{\link{KDNorm}},
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-\code{\link{meanScaledHydropathy}()},
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-\code{\link{scaledHydropathyLocal}()}
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-
135 77
 Other scaled hydropathy functions: 
136 78
 \code{\link{KDNorm}},
137 79
 \code{\link{meanScaledHydropathy}()},
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Vignette and Documentation Updates

Proofreading and updating documentation for the package

WilliamMc authored on 17/06/2020 18:50:56
Showing1 changed files
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@@ -12,7 +12,7 @@ scaledHydropathyGlobal(sequence, plotResults = FALSE, proteinName = NA, ...)
12 12
 \item{sequence}{amino acid sequence as a single character string
13 13
 or vector of single characters.
14 14
 It also supports a single character string that specifies
15
-the locaion of a .fasta or .fa file.}
15
+the path to a .fasta or .fa file.}
16 16
 
17 17
 \item{plotResults}{logical value, FALSE by default.
18 18
 If \code{plotResults = TRUE} a plot will be the output.
... ...
@@ -32,7 +32,7 @@ if \code{plotResults = TRUE}, a graphical representation data.
32 32
 
33 33
 if \code{plotResults = TRUE}, a graphical representation data.
34 34
   Average is shown by the horizontal line.
35
-  If \code{plotResults = FALSE}, a dataframe is reported
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+  If \code{plotResults = FALSE}, a data frame is reported
36 36
   with each amino acid and each residue value shown.
37 37
   Score for each residue shown in the column "Hydropathy".
38 38
 }
... ...
@@ -44,7 +44,7 @@ This is used to calculate the scaled hydropathy of an amino acid
44 44
 
45 45
 This is used to calculate the scaled hydropathy of an amino acid
46 46
   sequence for each residue in the sequence.
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-  The output is either a dataframe or graph
47
+  The output is either a data frame or graph
48 48
   showing the matched scores for each residue along the sequence.
49 49
 }
50 50
 \examples{
Browse code

Added example documentation and combined similar scripts into the same file

WilliamMc authored on 05/06/2020 22:41:26
Showing1 changed files
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@@ -1,9 +1,11 @@
1 1
 % Generated by roxygen2: do not edit by hand
2
-% Please edit documentation in R/scaledHydropathyGlobal.R
2
+% Please edit documentation in R/scaledHydropathy.R
3 3
 \name{scaledHydropathyGlobal}
4 4
 \alias{scaledHydropathyGlobal}
5 5
 \title{Protein Scaled Hydropathy Calculations}
6 6
 \usage{
7
+scaledHydropathyGlobal(sequence, plotResults = FALSE, proteinName = NA, ...)
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+
7 9
 scaledHydropathyGlobal(sequence, plotResults = FALSE, proteinName = NA, ...)
8 10
 }
9 11
 \arguments{
... ...
@@ -22,6 +24,12 @@ optional setting to include the name in the plot title.}
22 24
 \item{...}{any additional parameters, especially those for plotting.}
23 25
 }
24 26
 \value{
27
+if \code{plotResults = TRUE}, a graphical representation data.
28
+  Average is shown by the horizontal line.
29
+  If \code{plotResults = FALSE}, a dataframe is reported
30
+  with each amino acid and each residue value shown.
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+  Score for each residue shown in the column "Hydropathy".
32
+
25 33
 if \code{plotResults = TRUE}, a graphical representation data.
26 34
   Average is shown by the horizontal line.
27 35
   If \code{plotResults = FALSE}, a dataframe is reported
... ...
@@ -31,9 +39,85 @@ if \code{plotResults = TRUE}, a graphical representation data.
31 39
 \description{
32 40
 This is used to calculate the scaled hydropathy of an amino acid
33 41
   sequence for each residue in the sequence.
34
-  Results are based on the
42
+  The output is either a dataframe or graph
43
+  showing the matched scores for each residue along the sequence.
44
+
45
+This is used to calculate the scaled hydropathy of an amino acid
46
+  sequence for each residue in the sequence.
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+  The output is either a dataframe or graph
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+  showing the matched scores for each residue along the sequence.
49
+}
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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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+##The path to the file as a character string
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+
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+exampleDF <- scaledHydropathyGlobal(aaString,
62
+                                    plotResults = FALSE)
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+head(exampleDF)
64
+
65
+exampleDF <- scaledHydropathyGlobal(aaVector,
66
+                                    plotResults = FALSE)
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+head(exampleDF)
68
+
69
+#plotResults = TRUE will output a ggplot
70
+\dontrun{
71
+  scaledHydropathyGlobal(aaString,
72
+                         plot = T)
73
+
74
+  #since it is a ggplot, you can change or annotate the plot
75
+  gg <- scaledHydropathyGlobal(aaVector,
76
+                               plot = T)
77
+  gg <- gg + ggplot2::ylab("Local Hydropathy")
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+  gg <- gg + ggplot2::geom_text(data = exampleDF,
79
+                                ggplot2::aes(label = AA,
80
+                                             y = Hydropathy + 0.1))
81
+  plot(gg)
82
+}
83
+#Amino acid sequences can be character strings
84
+aaString <- "ACDEFGHIKLMNPQRSTVWY"
85
+#Amino acid sequences can also be character vectors
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+aaVector <- c("A", "C", "D", "E", "F",
87
+              "G", "H", "I", "K", "L",
88
+           "M", "N", "P", "Q", "R",
89
+           "S", "T", "V", "W", "Y")
90
+#Alternativly, .fasta files can also be used by providing
91
+##The path to the file as a character string
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+
93
+exampleDF <- scaledHydropathyGlobal(aaString,
94
+                                    plotResults = FALSE)
95
+head(exampleDF)
96
+
97
+exampleDF <- scaledHydropathyGlobal(aaVector,
98
+                                    plotResults = FALSE)
99
+head(exampleDF)
100
+
101
+#plotResults = TRUE will output a ggplot
102
+\dontrun{
103
+  scaledHydropathyGlobal(aaString,
104
+                         plot = T)
105
+
106
+  #since it is a ggplot, you can change or annotate the plot
107
+  gg <- scaledHydropathyGlobal(aaVector,
108
+                               plot = T)
109
+  gg <- gg + ggplot2::ylab("Local Hydropathy")
110
+  gg <- gg + ggplot2::geom_text(data = exampleDF,
111
+                                ggplot2::aes(label = AA,
112
+                                             y = Hydropathy + 0.1))
113
+  plot(gg)
114
+}
35 115
 }
36 116
 \references{
117
+Kyte, J., & Doolittle, R. F. (1982). A simple method for
118
+  displaying the hydropathic character of a protein.
119
+  Journal of molecular biology, 157(1), 105-132.
120
+
37 121
 Kyte, J., & Doolittle, R. F. (1982). A simple method for
38 122
   displaying the hydropathic character of a protein.
39 123
   Journal of molecular biology, 157(1), 105-132.
... ...
@@ -41,6 +125,13 @@ Kyte, J., & Doolittle, R. F. (1982). A simple method for
41 125
 \seealso{
42 126
 \code{\link{KDNorm}} for residue values.
43 127
 
128
+\code{\link{KDNorm}} for residue values.
129
+
130
+Other scaled hydropathy functions: 
131
+\code{\link{KDNorm}},
132
+\code{\link{meanScaledHydropathy}()},
133
+\code{\link{scaledHydropathyLocal}()}
134
+
44 135
 Other scaled hydropathy functions: 
45 136
 \code{\link{KDNorm}},
46 137
 \code{\link{meanScaledHydropathy}()},
Browse code

Initial commit

WilliamMc authored on 13/05/2020 00:45:34
Showing1 changed files
1 1
new file mode 100644
... ...
@@ -0,0 +1,49 @@
1
+% Generated by roxygen2: do not edit by hand
2
+% Please edit documentation in R/scaledHydropathyGlobal.R
3
+\name{scaledHydropathyGlobal}
4
+\alias{scaledHydropathyGlobal}
5
+\title{Protein Scaled Hydropathy Calculations}
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+\usage{
7
+scaledHydropathyGlobal(sequence, plotResults = FALSE, proteinName = NA, ...)
8
+}
9
+\arguments{
10
+\item{sequence}{amino acid sequence as a single character string
11
+or vector of single characters.
12
+It also supports a single character string that specifies
13
+the locaion of a .fasta or .fa file.}
14
+
15
+\item{plotResults}{logical value, FALSE by default.
16
+If \code{plotResults = TRUE} a plot will be the output.
17
+If \code{plotResults = FALSE} the output is a data frame for each residue.}
18
+
19
+\item{proteinName}{character string with length = 1.
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+optional setting to include the name in the plot title.}
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+
22
+\item{...}{any additional parameters, especially those for plotting.}
23
+}
24
+\value{
25
+if \code{plotResults = TRUE}, a graphical representation data.
26
+  Average is shown by the horizontal line.
27
+  If \code{plotResults = FALSE}, a dataframe is reported
28
+  with each amino acid and each residue value shown.
29
+  Score for each residue shown in the column "Hydropathy".
30
+}
31
+\description{
32
+This is used to calculate the scaled hydropathy of an amino acid
33
+  sequence for each residue in the sequence.
34
+  Results are based on the
35
+}
36
+\references{
37
+Kyte, J., & Doolittle, R. F. (1982). A simple method for
38
+  displaying the hydropathic character of a protein.
39
+  Journal of molecular biology, 157(1), 105-132.
40
+}
41
+\seealso{
42
+\code{\link{KDNorm}} for residue values.
43
+
44
+Other scaled hydropathy functions: 
45
+\code{\link{KDNorm}},
46
+\code{\link{meanScaledHydropathy}()},
47
+\code{\link{scaledHydropathyLocal}()}
48
+}
49
+\concept{scaled hydropathy functions}