Fragman: Fragment Analysis in R
Version 1.0.7

Performs fragment analysis using genetic data coming from capillary electrophoresis machines. These are files with FSA extension which stands for FASTA-type file, and .txt files from Beckman CEQ 8000 system, both contain DNA fragment intensities read by machinery. In addition to visualization, it performs automatic scoring of SSRs (Sample Sequence Repeats; a type of genetic marker very common across the genome) and other type of PCR markers (standing for Polymerase Chain Reaction) in biparental populations such as F1, F2, BC (backcross), and diversity panels (collection of genetic diversity).

AuthorGiovanny Covarrubias-Pazaran, Luis Diaz-Garcia, Brandon Schlautman, Walter Salazar, Juan Zalapa.
Date of publication2016-09-01 19:36:53
MaintainerGiovanny Covarrubias-Pazaran <covarrubiasp@wisc.edu>
LicenseGPL-3
Version1.0.7
URL http://www.wisc.edu
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("Fragman")

Getting started

Package overview

Popular man pages

find.ladder: Ladder detection by correlation or confidence intervals
Fragman-package: Fragment analysis and automatic scoring
get.scores: complementary tools
lapply_pb: complementary tools for Fragman
overview: Assesing several plants with an overview
score.easy: Fragment analysis scoring
threshs: Customizing thresholds
See all...

All man pages Function index File listing

Man pages

arrange.jm: Arrange data converted to joinmap code into a joinmap...
best.layout: complementary tools for layout
big.peaks.col: Peak search by first derivatives
detect.ladder: Ladder detection by correlation or confidence intervals
find.ladder: Ladder detection by correlation or confidence intervals
Fragman-package: Fragment analysis and automatic scoring
get.scores: complementary tools
homogenize.to.parentals: complementary tools
homo.panel: complementary tools
jm.conv: Scores to JoinMap converter
ladder.corrector: Ladder corrector attached to R environment
ladder.info.attach: Ladder detection and attachment to R environment
lapply_pb: complementary tools for Fragman
letter.to.jm: Letter to JoinMap code converter
my.plants: Cranberry biparental population
num.to.lett: Number to Letter code converter
overview: Assesing several plants with an overview
overview2: Assesing several plants with an overview
pullup: Applying pullup to channels/colors
read.abif: Read ABIF formatted files
reals: Finding the real peaks
saturate: Checking and correcting saturated peaks
score.easy: Fragment analysis scoring
separate: Separating peaks by a shift window
storing.inds: Extracting channel information
threshs: Customizing thresholds
transfft: Applying the fourier transformation to a data frame
transp: Creating color with transparency

Functions

Fragman Man page
arrange.jm Man page Source code
best.layout Man page Source code
big.peaks.col Man page Source code
detect.ladder Man page Source code
find.ladder Man page Source code
get.scores Man page Source code
homo.panel Man page Source code
homogenize.to.parentals Man page Source code
jm.conv Man page Source code
ladder.corrector Man page Source code
ladder.info.attach Man page Source code
lapply_pb Man page Source code
letter.to.jm Man page Source code
my.plants Man page
num.to.lett Man page Source code
onAttach Source code
overview Man page Source code
overview2 Man page Source code
pullup Man page Source code
read.abif Man page Source code
reals Man page Source code
saturate Man page Source code
score.easy Man page Source code
separate Man page Source code
storing.inds Man page Source code
threshs Man page Source code
transfft Man page Source code
transp Man page Source code

Files

inst
inst/CITATION
NAMESPACE
data
data/datalist
data/my.plants.RData
R
R/homogenize.to.parentals.R
R/overview.R
R/lapply_pb.R
R/letter.to.jm.R
R/threshs.R
R/ladder.info.attach.R
R/Fragma-internal.R
R/homo.panel.R
R/ladder.corrector.R
R/reals.R
R/pullup.R
R/get.scores.R
R/detect.ladder.R
R/best.layout.R
R/jm.conv.R
R/big.peaks.col.R
R/saturate.R
R/transfft.R
R/read.abif.R
R/transp.R
R/num.to.lett.R
R/storing.inds.R
R/arrange.jm.R
R/score.easy.R
R/overview2.R
R/separate.R
R/find.ladder.R
MD5
DESCRIPTION
man
man/reals.Rd
man/arrange.jm.Rd
man/transfft.Rd
man/overview.Rd
man/homogenize.to.parentals.Rd
man/Fragman-package.Rd
man/saturate.Rd
man/num.to.lett.Rd
man/lapply_pb.Rd
man/separate.Rd
man/best.layout.Rd
man/ladder.info.attach.Rd
man/big.peaks.col.Rd
man/transp.Rd
man/read.abif.Rd
man/jm.conv.Rd
man/score.easy.Rd
man/pullup.Rd
man/detect.ladder.Rd
man/ladder.corrector.Rd
man/threshs.Rd
man/overview2.Rd
man/my.plants.Rd
man/get.scores.Rd
man/storing.inds.Rd
man/homo.panel.Rd
man/find.ladder.Rd
man/letter.to.jm.Rd
Fragman documentation built on May 19, 2017, 2:37 p.m.

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