Fragman: Fragment Analysis in R

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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).

Author
Giovanny Covarrubias-Pazaran, Luis Diaz-Garcia, Brandon Schlautman, Walter Salazar, Juan Zalapa.
Date of publication
2016-09-01 19:36:53
Maintainer
Giovanny Covarrubias-Pazaran <covarrubiasp@wisc.edu>
License
GPL-3
Version
1.0.7
URLs

View on CRAN

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

Files in this package

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