README.md

In douglasgscofield/readGenalex: Read, Write, Manipulate and Convert GenAlEx-Format Genotype Files

readGenalex

An R package for reading data files in GenAlEx format, as exported from Excel as a delimited text file, into an annotated data.frame of class 'genalex', and manipulate it in that form. Several functions are provided for accessing, manipulating, and printing this data. GenAlEx and its documentation are available at http://biology-assets.anu.edu.au/GenAlEx.

The most recent release 1.0 (now on CRAN) introduces the S3 class 'genalex', and implements the functionality of this package by defining an S3 class 'genalex' that is shared with data.frame.

Release version 1.0.9000

The development version is hosted on Github and can always be installed via:

> install.packages("devtools")
> devtools::install_github("douglasgscofield/readGenalex")

Using the package

readGenalex 1.0 can be installed through CRAN:

> install.packages("readGenalex")

Class genalex is an annotated data frame with attributes containing additional information specified by the user:

> library(readGenalex)
> data(Qagr_adult_genotypes)
> head(Qagr_adult_genotypes)
  AdultMomFamily     Site 0c11 0c11.2 0c19 0c19.2 Oe09 Oe09.2 0i01 0i01.2 0m05
1           2201 Sedgwick  215    215  226    244  190    192  204    206  210
2           2202 Sedgwick  213    217  238    238  190    192  204    204  210
3           2203 Sedgwick  213    215  234    240  190    192  196    206  216
4           2204 Sedgwick  213    213  234    234  186    192  196    204  210
5           2205 Sedgwick  213    217  222    238  190    194  204    204  210
6           2206 Sedgwick  213    213  226    240  194    194  196    204  202
  0m05.2 0m07 0m07.2 1c06 1c06.2 1c08 1c08.2 1f02 1f02.2 1g13 1g13.2
1    210  199    199  238    242  273    273  190    190  189    191
2    222  199    205  244    244  273    273  190    190  185    187
3    220  199    199  234    234  273    273  190    190  189    189
4    212  199    201  234    236  269    273  190    190  187    191
5    216  201    205  236    242  273    273  180    190  185    187
6    206  201    203  240    242  271    273  190    190  185    185
> class(Qagr_adult_genotypes)
[1] "genalex"    "data.frame"
> attributes(Qagr_adult_genotypes)
$names
 [1] "AdultMomFamily" "Site"           "0c11"           "0c11.2"
 [5] "0c19"           "0c19.2"         "Oe09"           "Oe09.2"
 [9] "0i01"           "0i01.2"         "0m05"           "0m05.2"
[13] "0m07"           "0m07.2"         "1c06"           "1c06.2"
[17] "1c08"           "1c08.2"         "1f02"           "1f02.2"
[21] "1g13"           "1g13.2"

$row.names
  [1]   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18
 [19]  19  20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36
 [37]  37  38  39  40  41  42  43  44  45  46  47  48  49  50  51  52  53  54
 [55]  55  56  57  58  59  60  61  62  63  64  65  66  67  68  69  70  71  72
 [73]  73  74  75  76  77  78  79  80  81  82  83  84  85  86  87  88  89  90
 [91]  91  92  93  94  95  96  97  98  99 100 101 102 103 104 105 106 107 108
[109] 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126
[127] 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144
[145] 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162
[163] 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180
[181] 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198
[199] 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216
[217] 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234
[235] 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252
[253] 253 254 255 256 257 258 259 260 261 262

$class
[1] "genalex"    "data.frame"

$n.loci
[1] 10

$ploidy
[1] 2

$n.samples
[1] 262

$n.pops
[1] 1

...

readGenalex reads GenAlEx-format data from a text file, and readGenalexExcel reads data from a specified worksheet of an Excel workbook of .xls or .xlsx format using the XLConnect package. Both functions read only the number of samples specified by the GenAlEX header, and only treat as genotypes the number of genotype columns implied by the GenAlEx header in concert with the stated ploidy level.

Because GenAlEx is an Excel plugin, readGenalex attempts to deal with various issues that may arise when exporting text files from Excel. readGenalex also tries to ignore extra tab characters that tools such as Excel can insert when exporting tab-delimited text, otherwise these could imply both additional columns and additional rows. Hopefully the latter is avoided by only reading the number of samples specified by the header.

If there are additional named columns to the right of the genotypes, these are read and stored in a data frame attached to the attribute extra.columns. The first column of the extra.columns data frame is the sample name (leftmost column from the genotypes, e.g., the id column from the above example). It attempts to ignore additional unnamed columns scattered amongst the named extra columns.

There are also corresponding writeGenalex and writeGenalexExcel functions.

Functions:

Function | Description -------- | ----------- readGenalex() | Read GenAlEx-format data from a text file readGenalexExcel() | Read GenAlEx-format data from a worksheet of an Excel workbook genalex() | Create a class 'genalex' object from constituent data as.genalex() | Generic function which converts a pre-1.0-style readGenalex data frame to class 'genalex', or converts a suitably-formatted data frame to class 'genalex'. Optionally it can determine structure implied by the data and update attributes to reflect that structure. writeGenalex() | Write a GenAlEx-format text file writeGenalexExcel() | Write a GenAlEx-format worksheet to an Excel workbook summary() | Prints a summary of the data set, a summary of the genotype data frame, and a summary of the extra columns, if any is.genalex() | Checks whether the object is class 'genalex', optionally does a deeper check to determine whether the structure described in the attributes matches the structure implied by the data as.data.frame() | Method to convert class 'genalex' to class 'data.frame', optionally all class 'genalex'-specific attributes are removed reducePloidy() | Reduce the ploidy to 1 by selecting the first allele of each locus dropLocus() | Drop named loci getPopulation() | Return genotypes of specific populations in object of class 'genalex' printGenotype() | Print genotypes of specific rows reorderLoci() | Reorder loci into a given order computeLocusColumns() | Return a vector of column numbers for specified loci replaceLocus() | Replace genotypes of specified locus getLocus() | Return genotypes of specified locus, optionally only for specific populations addLocus() | Add genotypes to an object of class 'genalex' extra() | Get or set extra.columns attribute ploidy() | Get ploidy attribute cbind() | Merge loci and extra data columns from two or more class 'genalex' objects rbind() | Merge samples from two or more class 'genalex' objects checkNullAlleles() | Compare genotypes against a set of reference genotypes to check for potential null (nonamplifying) alleles writeGenepop()| Write class 'genalex' object in Genepop format as.genetics() | Convert class 'genalex' object to a data frame with genotypes encoded using class genotype (unphased) or class haplotype (phased) from package genetics splitGenotypes() | Split genotypes encoded as 101/107 into separate columns of a data frame, suitable for further use with genalex() joinGenotypes() | Join class 'genalex' (or other class) genotypes into a single column as.loci.genalex | Extends the as.loci generic from the pegas package to convert class 'genalex' to class 'loci' as.genalex.loci | Converts an object of class 'loci' from the pegas package to class 'genalex'

Datasets

The package also provides two data sets as class 'genalex' objects that can be loaded with data:

• Qagr_adult_genotypes: Coast live oak (Quercus agrifolia) adult microsatellite genotypes, holding 10-locus diploid microsatellite genotypes of 262 adult coast live oak trees from Sedgwick Reserve, Santa Barbara County, California, USA
• Qagr_pericarp_genotypes: Coast live oak (Quercus agrifolia) pericarp microsatellite genotypes, holding 10-locus diploid microsatellite genotypes of 568 pericarps (outer seed coats) from coast live oak acorns collected from 17 acorn woodpecker (Melanerpes formicivorus) granaries at Sedgwick Reserve, Santa Barbara County, California, USA

These data sets are also available at the Dryad Data Repository, http://datadryad.org/resource/doi:10.5061/dryad.40kq7.

Several papers have been published with these data. If using them, please cite the original paper as well as the data:

Scofield DG, Smouse PE, Karubian J, Sork VL (2012) Use of alpha, beta, and gamma diversity measures to characterize seed dispersal by animals. The American Naturalist 180(6): 719-732. http://dx.doi.org/10.1086/668202

Scofield DG, Smouse PE, Karubian J, Sork VL (2012) Data from: Use of alpha, beta, and gamma diversity measures to characterize seed dispersal by animals. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.40kq7

douglasgscofield/readGenalex documentation built on May 15, 2019, 10:43 a.m.