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Fragman (version 1.0.8)

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 .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).

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Version

Install

install.packages('Fragman')

Monthly Downloads

254

Version

1.0.8

License

GPL-3

Maintainer

Giovanny CovarrubiasPazaran

Last Published

December 3rd, 2017

Functions in Fragman (1.0.8)

get.scores

complementary tools
homo.panel

complementary tools
pullup

Applying pullup to channels/colors
read.abif

Read ABIF formatted files
homogenize.to.parentals

complementary tools
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
arrange.jm

Arrange data converted to joinmap code into a joinmap readable file
transfft

Applying the fourier transformation to a data frame
transp

Creating color with transparency
reals

Finding the real peaks
saturate

Checking and correcting saturated peaks
overview

Assesing several plants with an overview
overview2

Assesing several plants with an overview
my.plants

Cranberry biparental population
best.layout

complementary tools for layout
big.peaks.col

Peak search by first derivatives
lapply_pb

complementary tools for Fragman
letter.to.jm

Letter to JoinMap code converter
num.to.lett

Number to Letter code converter
score.easy

Fragment analysis scoring
separate

Separating peaks by a shift window
storing.inds

Extracting channel information
threshs

Customizing thresholds
jm.conv

Scores to JoinMap converter
ladder.corrector

Ladder corrector attached to R environment
ladder.info.attach

Ladder detection and attachment to R environment