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Fragman (version 1.0.9)

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

247

Version

1.0.9

License

GPL-3

Last Published

January 14th, 2018

Functions in Fragman (1.0.9)

get.scores

complementary tools
homo.panel

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
homogenize.to.parentals

complementary tools
jm.conv

Scores to JoinMap converter
overview

Assesing several plants with an overview
overview2

Assesing several plants with an overview
best.layout

complementary tools for layout
big.peaks.col

Peak search by first derivatives
lapply_pb

complementary tools for Fragman
plot.fsa_stored

plot form fsa files stored with storing.inds
read.abif

Read ABIF formatted files
reals

Finding the real peaks
pullup

Applying pullup to channels/colors
letter.to.jm

Letter to JoinMap code converter
ladder.corrector

Ladder corrector attached to R environment
ladder.info.attach

Ladder detection and attachment to R environment
my.plants

Cranberry biparental population
num.to.lett

Number to Letter code converter
transp

Creating color with transparency
saturate

Checking and correcting saturated peaks
score.markers

Fragment analysis scoring
threshs

Customizing thresholds
transfft

Applying the fourier transformation to a data frame
separate

Separating peaks by a shift window
storing.inds

Extracting channel information