shubham1637 authored on 04/02/2020 16:29:02
| ... | ... |
@@ -6,7 +6,13 @@ |
| 6 | 6 |
\alias{AffineAlignObj}
|
| 7 | 7 |
\title{An S4 object for class AffineAlignObj}
|
| 8 | 8 |
\description{
|
| 9 |
-An S4 object for class AffineAlignObj |
|
| 9 |
+s is a point-wise similarity matrix between signalA and signalB. |
|
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+Intermediate matrices M,A,B are calculated from s for affine-alignment. Each cell of the Traceback |
|
| 11 |
+matrix has coordinate of its parent cell. path matrix is a binary matrix with ones indicating path |
|
| 12 |
+of maximum cumulative score. |
|
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+GapOpen and GapExten are gap-opening and gap-extension penalties used by affine alignment algorithm. |
|
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+indexA_aligned and indexB_aligned are aligned indices of signalA and SignalB. The cumulative |
|
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+alignment score is in score vector. |
|
| 10 | 16 |
} |
| 11 | 17 |
\seealso{
|
| 12 | 18 |
\code{\link{doAffineAlignmentCpp}}
|
| ... | ... |
@@ -16,6 +22,6 @@ Shubham Gupta, \email{shubh.gupta@mail.utoronto.ca}
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| 16 | 22 |
|
| 17 | 23 |
ORCID: 0000-0003-3500-8152 |
| 18 | 24 |
|
| 19 |
-License: (c) Author (2019) + MIT |
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+License: (c) Author (2019) + GPL-3 |
|
| 20 | 26 |
Date: 2019-12-14 |
| 21 | 27 |
} |
| ... | ... |
@@ -6,7 +6,8 @@ |
| 6 | 6 |
\alias{AffineAlignObjLight}
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| 7 | 7 |
\title{An S4 object for class AffineAlignObj. It only contains aligned indices.}
|
| 8 | 8 |
\description{
|
| 9 |
-An S4 object for class AffineAlignObj. It only contains aligned indices. |
|
| 9 |
+indexA_aligned and indexB_aligned are aligned indices of signalA and SignalB. The cumulative |
|
| 10 |
+alignment score is in score vector. |
|
| 10 | 11 |
} |
| 11 | 12 |
\seealso{
|
| 12 | 13 |
\code{\link{doAffineAlignmentCpp}}
|
| ... | ... |
@@ -16,6 +17,6 @@ Shubham Gupta, \email{shubh.gupta@mail.utoronto.ca}
|
| 16 | 17 |
|
| 17 | 18 |
ORCID: 0000-0003-3500-8152 |
| 18 | 19 |
|
| 19 |
-License: (c) Author (2019) + MIT |
|
| 20 |
+License: (c) Author (2019) + GPL-3 |
|
| 20 | 21 |
Date: 2019-12-14 |
| 21 | 22 |
} |
| ... | ... |
@@ -6,7 +6,11 @@ |
| 6 | 6 |
\alias{AffineAlignObjMedium}
|
| 7 | 7 |
\title{An S4 object for class AffineAlignObj. It only contains similarity matrix and aligned indices.}
|
| 8 | 8 |
\description{
|
| 9 |
-An S4 object for class AffineAlignObj. It only contains similarity matrix and aligned indices. |
|
| 9 |
+s is a point-wise similarity matrix between signalA and signalB. |
|
| 10 |
+path matrix is a binary matrix with ones indicating path of maximum cumulative score. |
|
| 11 |
+GapOpen and GapExten are gap-opening and gap-extension penalties used by affine alignment algorithm. |
|
| 12 |
+indexA_aligned and indexB_aligned are aligned indices of signalA and SignalB. The cumulative |
|
| 13 |
+alignment score is in score vector. |
|
| 10 | 14 |
} |
| 11 | 15 |
\seealso{
|
| 12 | 16 |
\code{\link{doAffineAlignmentCpp}}
|
| ... | ... |
@@ -16,6 +20,6 @@ Shubham Gupta, \email{shubh.gupta@mail.utoronto.ca}
|
| 16 | 20 |
|
| 17 | 21 |
ORCID: 0000-0003-3500-8152 |
| 18 | 22 |
|
| 19 |
-License: (c) Author (2019) + MIT |
|
| 23 |
+License: (c) Author (2019) + GPL-3 |
|
| 20 | 24 |
Date: 2019-12-14 |
| 21 | 25 |
} |
| ... | ... |
@@ -6,7 +6,13 @@ |
| 6 | 6 |
\alias{AlignObj}
|
| 7 | 7 |
\title{An S4 object for class AlignObj}
|
| 8 | 8 |
\description{
|
| 9 |
-An S4 object for class AlignObj |
|
| 9 |
+s is a point-wise similarity matrix between signalA and signalB. |
|
| 10 |
+Intermediate matrices M is calculated from s for alignment. Each cell of the Traceback |
|
| 11 |
+matrix has coordinate of its parent cell. path matrix is a binary matrix with ones indicating path |
|
| 12 |
+of maximum cumulative score. |
|
| 13 |
+GapOpen and GapExten are gap-opening and gap-extension penalties used by alignment algorithm. They |
|
| 14 |
+must be the same. indexA_aligned and indexB_aligned are aligned indices of signalA and SignalB. |
|
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+The cumulative alignment score is in score vector. |
|
| 10 | 16 |
} |
| 11 | 17 |
\seealso{
|
| 12 | 18 |
\code{\link{doAlignmentCpp}}
|
| ... | ... |
@@ -16,6 +22,6 @@ Shubham Gupta, \email{shubh.gupta@mail.utoronto.ca}
|
| 16 | 22 |
|
| 17 | 23 |
ORCID: 0000-0003-3500-8152 |
| 18 | 24 |
|
| 19 |
-License: (c) Author (2019) + MIT |
|
| 25 |
+License: (c) Author (2019) + GPL-3 |
|
| 20 | 26 |
Date: 2019-12-14 |
| 21 | 27 |
} |
| ... | ... |
@@ -11,7 +11,8 @@ |
| 11 | 11 |
\item{intensity}{Intensity of signal for the transition}
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| 12 | 12 |
}} |
| 13 | 13 |
\source{
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-data-raw/test_GenerateData.R has source code. |
|
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+Raw files are downloaded from [Peptide Atlas](http://www.peptideatlas.org/PASS/PASS01508). |
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+data-raw/test_GenerateData.R has [source code](https://github.com/shubham1637/DIAlignR/tree/master/data-raw). |
|
| 15 | 16 |
} |
| 16 | 17 |
\usage{
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| 17 | 18 |
XIC_QFNNTDIVLLEDFQK_3_DIAlignR |
| ... | ... |
@@ -9,9 +9,9 @@ areaIntegrator(l1, leftIdx, rightIdx) |
| 9 | 9 |
\arguments{
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| 10 | 10 |
\item{l1}{(list) A list of vectors. All vectors must be of same length.}
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| 11 | 11 |
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-\item{leftIdx}{(numeric) Left index of the boundary.}
|
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+\item{leftIdx}{(numeric) Left index (0-based) of the boundary.}
|
|
| 13 | 13 |
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-\item{rightIdx}{(numeric) Right index of the boundary.}
|
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+\item{rightIdx}{(numeric) Right index (0-based) of the boundary.}
|
|
| 15 | 15 |
} |
| 16 | 16 |
\value{
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| 17 | 17 |
area (numeric). |
| ... | ... |
@@ -19,6 +19,10 @@ area (numeric). |
| 19 | 19 |
\description{
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| 20 | 20 |
This function sums all the intensities between left-index and right-index. |
| 21 | 21 |
} |
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+\examples{
|
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+l1 <- list(1:10, 1:10, 1:10) |
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+areaIntegrator(l1, leftIdx = 4, rightIdx = 6) # 54 |
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+} |
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| 22 | 26 |
\author{
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| 23 | 27 |
Shubham Gupta, \email{shubh.gupta@mail.utoronto.ca}
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| 24 | 28 |
ORCID: 0000-0003-3500-8152 |
| ... | ... |
@@ -27,23 +27,23 @@ Match=10; MisMatch=-2 |
| 27 | 27 |
seq1 = "GCAT"; seq2 = "CAGTG" |
| 28 | 28 |
s <- getSeqSimMatCpp(seq1, seq2, Match, MisMatch) |
| 29 | 29 |
objAffine_Global <- doAffineAlignmentCpp(s, 22, 7, FALSE) |
| 30 |
-objAffine_Global@score # -2 -4 -6 4 -18 |
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+slot(objAffine_Global, "score") # -2 -4 -6 4 -18 |
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| 31 | 31 |
objAffine_Olap <- doAffineAlignmentCpp(s, 22, 7, TRUE) |
| 32 |
-objAffine_Olap@score # 0 10 20 18 18 18 |
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+slot(objAffine_Olap, "score") # 0 10 20 18 18 18 |
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| 33 | 33 |
|
| 34 | 34 |
Match=10; MisMatch=-2 |
| 35 | 35 |
seq1 = "CAT"; seq2 = "CAGTG" |
| 36 | 36 |
s <- getSeqSimMatCpp(seq1, seq2, Match, MisMatch) |
| 37 | 37 |
objAffine_Global <- doAffineAlignmentCpp(s, 22, 7, FALSE) |
| 38 |
-objAffine_Global@score # 10 20 -2 -9 -11 |
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+slot(objAffine_Global, "score") # 10 20 -2 -9 -11 |
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| 39 | 39 |
objAffine_Olap <- doAffineAlignmentCpp(s, 22, 7, TRUE) |
| 40 |
-objAffine_Olap@score # 10 20 18 18 18 |
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+slot(objAffine_Olap, "score") # 10 20 18 18 18 |
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| 41 | 41 |
|
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Match=10; MisMatch=-2 |
| 43 | 43 |
seq1 = "CA"; seq2 = "AG" |
| 44 | 44 |
s <- getSeqSimMatCpp(seq1, seq2, Match, MisMatch) |
| 45 | 45 |
objAffine_Global <- doAffineAlignmentCpp(s, 22, 7, FALSE) |
| 46 |
-objAffine_Global@simScore_forw # -4 |
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+slot(objAffine_Global, "simScore_forw") # -4 |
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| 47 | 47 |
} |
| 48 | 48 |
\author{
|
| 49 | 49 |
Shubham Gupta, \email{shubh.gupta@mail.utoronto.ca}
|
| ... | ... |
@@ -25,17 +25,17 @@ Match=10; MisMatch=-2 |
| 25 | 25 |
seq1 = "GCAT"; seq2 = "CAGTG" |
| 26 | 26 |
s <- getSeqSimMatCpp(seq1, seq2, Match, MisMatch) |
| 27 | 27 |
obj_Global <- doAlignmentCpp(s, 22, FALSE) |
| 28 |
-obj_Global@score # -2 -4 -6 4 -18 |
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+slot(obj_Global, "score") # -2 -4 -6 4 -18 |
|
| 29 | 29 |
obj_Olap <- doAlignmentCpp(s, 22, TRUE) |
| 30 |
-obj_Olap@score # 0 10 20 18 18 18 |
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+slot(obj_Olap, "score") # 0 10 20 18 18 18 |
|
| 31 | 31 |
|
| 32 | 32 |
Match=1; MisMatch=-1 |
| 33 | 33 |
seq1 = "TTTC"; seq2 = "TGC" |
| 34 | 34 |
s <- getSeqSimMatCpp(seq1, seq2, Match, MisMatch) |
| 35 | 35 |
obj_Global <- doAlignmentCpp(s, 2, FALSE) |
| 36 |
-obj_Global@optionalPaths |
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+slot(obj_Global, "optionalPaths") |
|
| 37 | 37 |
matrix(data = c(1,1,1,1,1,1,1,1,1,2,1,2,1,3,3,1,1,3,6,3), nrow = 5, ncol =4, byrow = TRUE) |
| 38 |
-obj_Global@M_forw |
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+slot(obj_Global, "M_forw") |
|
| 39 | 39 |
matrix(data = c(0,-2,-4,-6,-2,-7,-22,-45,-4,-20,-72,-184,-6,-41,-178,-547,-8,-72,-366,-1274), |
| 40 | 40 |
nrow = 5, ncol =4, byrow = TRUE) |
| 41 | 41 |
} |
| ... | ... |
@@ -24,7 +24,7 @@ and second column indicates intensity.} |
| 24 | 24 |
A plot to the current device. |
| 25 | 25 |
} |
| 26 | 26 |
\description{
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-AlignObjOutput is the output from getAlignObjs fucntion. |
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+AlignObj is the output from getAlignObjs fucntion. This function prepares ggplot objects from AlignObj. |
|
| 28 | 28 |
} |
| 29 | 29 |
\examples{
|
| 30 | 30 |
dataPath <- system.file("extdata", package = "DIAlignR")
|
| ... | ... |
@@ -41,7 +41,7 @@ Shubham Gupta, \email{shubh.gupta@mail.utoronto.ca}
|
| 41 | 41 |
|
| 42 | 42 |
ORCID: 0000-0003-3500-8152 |
| 43 | 43 |
|
| 44 |
-License: (c) Author (2019) + MIT |
|
| 44 |
+License: (c) Author (2019) + GPL-3 |
|
| 45 | 45 |
Date: 2019-12-13 |
| 46 | 46 |
} |
| 47 | 47 |
\keyword{internal}
|
| ... | ... |
@@ -20,7 +20,8 @@ |
| 20 | 20 |
\item{transition_ids}{Transition IDs (chromatogram IDs) of the feature}
|
| 21 | 21 |
}} |
| 22 | 22 |
\source{
|
| 23 |
-data-raw/test_GenerateData.R has source code. |
|
| 23 |
+Raw files are downloaded from [Peptide Atlas](http://www.peptideatlas.org/PASS/PASS01508). |
|
| 24 |
+data-raw/test_GenerateData.R has [source code](https://github.com/shubham1637/DIAlignR/tree/master/data-raw). |
|
| 24 | 25 |
} |
| 25 | 26 |
\usage{
|
| 26 | 27 |
oswFiles_DIAlignR |