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Fragman (version 1.0.1)

Fragment Analysis in R

Description

Performs fragment analysis using genetic data coming from capillary electrophoresis machines. These are files with FSA extension which stands for FASTA-type file and contains 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).

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Version

Install

install.packages('Fragman')

Monthly Downloads

440

Version

1.0.1

License

GPL-3

Maintainer

Giovanny CovarrubiasPazaran

Last Published

September 22nd, 2015

Functions in Fragman (1.0.1)

detect.ladder

Ladder detection by correlation or confidence intervals
find.ladder

Ladder detection by correlation or confidence intervals
get.scores

complementary tools
overview2

Assesing several plants with an overview
transp

Creating color with transparency
overview

Assesing several plants with an overview
score.easy

Fragment analysis scoring
big.peaks.col

Peak search by first derivatives
Fragman-package

Fragment analysis and automatic scoring
saturate

Checking and correcting saturated peaks
transfft

Applying the fourier transformation to a data frame
reals

Finding the real peaks
arrange.jm

Arrange data converted to joinmap code into a joinmap readable file
letter.to.jm

Letter to JoinMap code converter
best.layout

complementary tools for layout
num.to.lett

Number to Letter code converter
separate

Separating peaks by a shift window
homo.panel

complementary tools
lapply_pb

complementary tools for Fragman
read.abif

Read ABIF formatted files
my.plants

Cranberry biparental population
threshs

Customizing thresholds
pullup

Applying pullup to channels/colors
homogenize.to.parentals

complementary tools
ladder.info.attach

Ladder detection and attachment to R environment
jm.conv

Scores to JoinMap converter
storing.inds

Extracting channel information