package ‘genomatic’ · 2013-08-29 · package ‘genomatic’ february 15, 2013 type package...

Package ‘genomatic’February 15, 2013

Type Package

Title Manages microsatellite projects. Creates 96-well maps,genotyping submission forms, rerun management, and import intostatistical software.

Version 0.0-7

Date 2010-01-05

Author Brian J. Knaus

Maintainer Brian J. Knaus <[email protected]>

Depends R (>= 2.9.2), tcltk

Description Manages DNA fragment analysis projects. Creates 96-wellmaps, genotyping submission forms, rerun management, and import to statistical software.

License GPL-2

Repository CRAN

Date/Publication 2012-10-29 08:58:49

NeedsCompilation no

R topics documented:abi_sub . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2allele_char . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3allele_hist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4allele_process . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4bin_by_num . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5bin_caller . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6bin_init . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7bin_score . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7cat_sorter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8condense . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

1

2 abi_sub

dup_checker . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10dup_replace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10filename2sample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11genobins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12genogui . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13genomatic2genalex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13genomatic2ntsys . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14genotyper2genomatic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15init_gmtc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15order_sample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16plater . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17plate_write . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18pop2indiv . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18pop_get . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19sample_sorter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Index 21

abi_sub Creates ABI submission forms

Description

Takes a 96-well plate and converts it into a submission form for ABI genotyping.

Usage

abi_sub(plate, fset, outfile)

Arguments

plate A 96-well plate of samples

fset filter set to be used

outfile Name of the outfile (ABI submission form) to be created

Details

This function takes a 96-well plate and converts it into an ABI format submission file. The welllocation is indicated. A sample name is created by concatenating the well and the sample name.The color number is indicated. The standard dye, dye set, and color info is set based on the colorinfo input by the user. A color comment is created by concatenating the sample name (with wellnumber), the color info, and the information provided in ‘loci\_cats.’ This is output to a commadelimited file which can be directly used by the ABI software or it can be opened with a spreadsheetand saved in a proprietary format.

Value

Returns a NULL.

allele_char 3

Author(s)

Brian J. Knaus <[email protected]> http://brianknaus.com

References

Knaus, B.J. In prep. Genomatic: an R package for DNA fragment analysis project management.

allele_char Characterizes bins

Description

Records the mean, standard deviation, minimum, maximum, and count for each allele in a locus.

Usage

allele_char(allele.v, allele.df)

Arguments

allele.v All the peaks for a locus.

allele.df an allele file containing bin mixima and minima in columns 8 and 9.

Details

Characterizes bins based on allele data. Alleles in allele.v are sorted from smallest to biggestand then sorted into bins based on the min and max included in allele.df. A mean is recordedand rounded to produce an allele name. Standard deviation, min, max, count and range are alsorecorded. Complete allele files are printed to file, one for each locus.

Value

returns a data.frame.

Author(s)


References


http://brianknaus.com


4 allele_process

allele_hist Creates histograms of alleles

Description

Creates hisograms of alleles with bins in alternating colors and non-bins in black.

Usage

allele_hist(gmtc.a, allele.df, xlim=NULL)

Arguments

gmtc.a Allelic data in the form of two columns from a genomatic file.

allele.df An allele file containing bin information for the locus

xlim A vector containing the minimum and maximum values for the x axis

Details

Creates hisograms of alleles with bins in alternating colors and non-bins in black.

Value

Prints histogram to graphical device.

Author(s)


References

Knaus, B.J. In prep. Genomatic: an R package for DNA fragment analysis project management

allele_process Processes alleles into bins

Description

Processes alleles into bins for the entire project. Descriptive plots and text output are created.

Usage

allele_process(gmtc, allele.l)


bin_by_num 5

Arguments

gmtc a genomatic data.frame.

allele.l a list where each element contains a genomatic allele file.

Details

Processes alleles into bins for characterization. Alleles are binned by the min and max provided incolumns 8 and 9 of each allele file. Histograms are created for each locus with alternating color toindicate bins. Range by count plots are provided to find bins that are unusually wide.

Value

Returns a NULL.

Author(s)


References


bin_by_num Graphical output of bin quality

Description

Graphical output of bin quality. Creates plots of bin width as a function number of peaks in the bin.

Usage

bin_by_num(locus, loci, ident = 0)

Arguments

locus allele characteristics produced ‘allele\_char’

loci a data.frame of locus names

ident flag to enable interactive identification of points when set to 1. Default is no.

Details

Graphical output of bin quality. Creates plots of bin width as a function number of peaks in thebin. A heavy line is plotted at one base pair and thinner lines are plotted at 1.1, 1.2, 1.3, and 1.4base pairs. It seems intuitive that a bin should not range more than a base pair, however experiencesuggests that bins that range more than a single base pair are frequently acceptable. This could bedue to error in the size calling (how close the peak is to a size standard), among capillary error(capillary quality may induce error), or other unforeseen issues.


6 bin_caller

Value

Returns a NULL.

Author(s)


References


bin_caller Bins peaks

Description

Uses allele characteristics to call bins.

Usage

bin_caller(locus, locus_char, ploid=2)

Arguments

locus a data.frame containing all the peaks to be binned

locus\_char a table output from ‘allele\_char’ containing characteristics of the alleles (mean,sd, etc.)

ploid describes whether allelic data is spread over one column (haploid) or two (diploid).

Details

Uses allele characteristics to call bins. If a particular peak does not fall within any of the bins it isflagged with an ’NA.’

Value

Returns a NULL.

Author(s)


References




bin_init 7

bin_init Initializes allele files

Description

Initializes allele files

Usage

bin_init(samples, gap=0.3)

Arguments

samples a genomatic file where column one contains populations, column 2 containsindividuals and subsequent columns contain allelic data, two columns per locus

gap defines the gap size required to start a new bin

Details

Initializes allele files. Writes a comma delimited allele file for each locus.

Value

Returns a NULL.

Author(s)


References


bin_score Automates bin scoring

Description

Automates the bin calling process

Usage

bin_score(plate, loci, outfile="_scored_gmtc.csv")


8 cat_sorter

Arguments

plate a 96-well plate of samples

loci a table of allele characteristics

outfile a name for an outfile

Details

Automates bin calling, extracting population info from the names, sorting the samples and writes atext output file.

Value

Returns a NULL.

Author(s)


References


cat_sorter Sorts categories to their sample

Description

This function takes the output from Genotyper export tables and sorts it into elements of a list whereeach element includes only one category (locus).

Usage

cat_sorter(gdata)

Arguments

gdata A data.frame which is input from a Genotyper table export.

Details

The output from the Genotyper table export will include one category (locus) per row and willtherefore include one sample on many rows. This function reformats this file so that each sampleoccupies only a single row and has many categores (loci).

Value

Returns a data.frame of scored data.


condense 9

Author(s)


References


condense Merges samples with multiple non-identical records

Description

Merges samples with multiple non-identical records, only removes NAs.

Usage

condense(gmtc)

Arguments

gmtc A genomatic data.frame.

Details

When a sample has been run more than once but for different loci (multiplexes) these multiplerecords can be combined without losing data, only NAs.

Value

Returns a genomatic data.frame.

Author(s)


References




10 dup_replace

dup_checker Checks for duplicate samples

Description

Checks a file for duplicates. Returns a sorted file containing duplicates.

Usage

dup_checker(samples)

Arguments

samples A data.frame containing your samples.

Details

Checks a file for duplicates. Returns a sorted file containing duplicates. Duplicates are sorted sothey appear next to each other. This file can then be manually sorted to that there is only one instanceof each sample. This file is subsequently used by the function ‘dup\_replace’ to remove duplicatesand replace them with a single instance.

Value

Retruns a data.frame of samples that appear more than once.

Author(s)


References


dup_replace Replaces duplicate samples with a single sample

Description

Uses the manually edited file created in ‘dup\_checker’ to remove duplicate samples in a data.frame.

Usage

dup_replace(all_samps, replace_samps)


filename2sample 11

Arguments

all_samps A data.frame of your entire dataset (including duplicates).

replace_samps A data.frame of samples created by ‘dup\_checker’ and manually edited so onlya single instance of each sample appears.

Details

Uses the manually edited file created in ‘dup\_checker’ to remove duplicate samples in a data.frame.The samples names in ‘replace\_samps’ are used to remove all instances of these names from‘all\_samps.’ ‘replace\_samps’ is then added to the dataset. Finally ‘order\_sample’ is used toorder the samples alpha-numericallly.

Value

Returns a data.frame that is sorted and includes no duplicates.

Author(s)


References


filename2sample Extracts sample names from file names

Description

Takes the field ’File.Name’ and extracts the sample name from it.

Usage

filename2sample(file.name)

Arguments

file.name A vector of File.Names.

Details

The file name is expected to follow the format specified in the function ‘plate\_write.’ An example is‘A10\_PUTR\_068\_01\_A10\_02.fsa’ where the sample name is ‘PUTR\_068\_01.’ This functionextracts this sample name assuming the character ‘\_’ delimits fields within ‘File.Name’ and returnsa data.frame containing just the sample name.


12 genobins

Value

A data.frame containing sample names.

Author(s)


References


genobins Remove peaks from files and leave bins

Description

Removes peak calls from files and leaves bin calls. Prepares for output to statistical software.

Usage

genobins(samples)

Arguments

samples a data.frame of samples containing peak calls and bin calls

Details

Removes peak calls from files and leaves bin calls. Prepares for output to statistical software.

Value

Returns a data.frame.

Author(s)


References




genogui 13

genogui Genomatic graphical user interface

Description

Graphical user interface designed to run genomatic functions.

Usage

genogui()

Arguments

genogui takes no arguments

Details

Graphical user interface designed to run genomatic functions.

Value

Returns nothing.

Author(s)


References


genomatic2genalex Converts data to GenAlEx format

Description

Converts data to GenAlEx format

Usage

genomatic2genalex(data, outfile)

Arguments

data a data.frame containing your data

outfile a name for your outfile


14 genomatic2ntsys

Details

Converts data to GenAlEx format. This software is convenient because it provides output to manyother formats. Therefore, even if you’re not interested in GenAlEx you might find it to be a conve-nient conversion tool. See http://www.anu.edu.au/BoZo/GenAlEx/ for information on GenAlEx.

Value

Returns a NULL.

Author(s)


References


genomatic2ntsys Converts data to NTSYSpc format

Description

Converts data to the NTYSYSpc format

Usage

genomatic2ntsys(samples, outfile)

Arguments

samples a data.frame of your dataoutfile a name for your outfile

Details

Converts data to the NTSysPC format. See http://www.exetersoftware.com/cat/ntsyspc/ntsyspc.htmlfor information on NTSYSpc. NTSYSpc is commercial software.

Value

Returns a NULL.

Author(s)


References




genotyper2genomatic 15

genotyper2genomatic Import genotyper tables

Description

Reformats data from the Genotyper table export format to the genomatic format.

Usage

genotyper2genomatic(gmtc, plate.l)

Arguments

gmtc A genomatic data.frame.

plate.l A list where each element is a plate of samples.

Details

This function reformats data from the Genotyper table export format to the genomatic format. Itcalls the functions ‘cat\_sorter’, ‘filename2sample’, ‘pop\_get’, and ‘order\_sample’ to accomplishthis.

Value

Returns a formatted data.frame.

Author(s)


References


init_gmtc Initializes a genomatic data.frame

Description

Initializes a genomatic data.frame.

Usage

init_gmtc(loci)


16 order_sample

Arguments

loci A data.frame of loci used in the project

Details

This function initializes a genomatic data.frame. This format is used throughout the genomaticprocess. A genomatic data.frame is specific to diploid organisms. The first coloumn is a populationcode. The second column is an individual code. All following columns are diploid loci in pairs. Forexample, columns three and four would contain locus one alleles a and b.

Value

Returns a genomatic data.frame.

Author(s)


References


order_sample Order samples alphanumerically

Description

Organizes the data alpha-numerically.

Usage

order_sample(data_df)

Arguments

data_df A data.frame of data where the first column is the sample name.

Details

A data.frame of data where the first column is the sample name. The data.frame is reordered alpha-numerically based on sample name.

Value

A data.frame.

Author(s)




plater 17

References


plater Organizes individual names into 96-well plates

Description

Organizes individual names into 96-well plates

Usage

plater(samps)

Arguments

samps A vector of individual names

Details

Takes a vector of individual names and organizes them into a matrix in the format of 96-well plates.

Value

Returns a list where each element is a 96-well plate of samples. Each element is a matrix of samples.

Author(s)


References



18 pop2indiv

plate_write Write 96-well maps

Description

A function that takes a list of 96-well plates and writes each to an individual comma delimited file.

Usage

plate_write(plates, prefix)

Arguments

plates A list where each element is a matrix representation of a 96-well plate withsamples.

prefix A prefix for you outfile names.

Details

This function takes a list of 96-well plates that has been created by the function ’plater’ (or is in thesame format) and saves each 96-well plate as a comma delimited file. Comma delimited files caneasily be imported into spreadsheets for further editing.

Value

Ruturns a NULL.

Author(s)


References


pop2indiv Population Name to Individual Name Conversion

Description

Takes population names and the respective sample size per population (n) and expands the popula-tion names to sample names of population\_name\_1, . . ., population\_name\_n.

Usage

pop2indiv(sites)


pop_get 19

Arguments

sites data.grame containing population names and sample sizes.

Details

The object ‘samps’ should be a vector of factors containing the population names. The object ‘n’should be a vector of integers containing population sample sizes in the same population order asthe object ‘samps.’

Value

returns a vector of character strings where each element is a population name and sample number(e.g., population\_name\_1, . . ., population\_name\_n).

Author(s)


References


pop_get Get populations from sample names

Description

Extracts the population name from a sample’s name

Usage

pop_get(data)

Arguments

data A data.frame of sample names where the sample names are in the first column.All subsequent columns are ignored.

Details

This function takes a data.frame of sample names which follows the format specified in the func-tion ‘filename2sample’. For example, the sample name ‘PUTR\_068\_01’ is from the population‘PUTR\_068.’ A data.frame consisting of one column which contains the population names is re-turned.

Value

A data.frame consisting of one column which contains the population names.


20 sample_sorter

Author(s)


References


sample_sorter Sorts data from separate lists into a data.frame

Description

Sorts data from separate lists into a data.frame

Usage

sample_sorter(samp_names, locus_l)

Arguments

samp_names a vector of sample names to sort all samples with

locus_l a list where each element contains data for a different locus

Details

Takes a vector of sample names and a list where each element in the list is a data.frame containiniga different locus and organizes this into a single data.frame.

Value

Returns a data.frame of sorted data.

Author(s)


References




Index

∗Topic manipabi_sub, 2allele_char, 3allele_hist, 4allele_process, 4bin_by_num, 5bin_caller, 6bin_init, 7bin_score, 7cat_sorter, 8condense, 9dup_checker, 10dup_replace, 10filename2sample, 11genobins, 12genogui, 13genomatic2genalex, 13genomatic2ntsys, 14genotyper2genomatic, 15init_gmtc, 15order_sample, 16plate_write, 18plater, 17pop2indiv, 18pop_get, 19sample_sorter, 20

pop_get (pop_get), 19

abi_sub, 2allele_char, 3allele_hist, 4allele_process, 4

bin_by_num, 5bin_caller, 6bin_init, 7bin_score, 7

cat_sorter, 8

condense, 9

dup_checker, 10dup_replace, 10

filename2sample, 11

genobins, 12genogui, 13genomatic2genalex, 13genomatic2ntsys, 14genotyper2genomatic, 15

init_gmtc, 15

order_sample, 16

plate_write, 18plater, 17pop2indiv, 18pop_get, 19

sample_sorter, 20

21

package ‘genomatic’ · 2013-08-29 · package ‘genomatic’ february 15, 2013 type package...

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