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Get.relabund
From mothur
The get.relabund command calculates the relative abundance of each otu in a sample. It outputs a .relabund file.
Contents |
Default Settings
mothur > make.shared(list=abrecovery.fn.list, group=abrecovery.groups) mothur > get.relabund(shared=abrecovery.fn.shared)
scale
The scale parameter allows you to select what scale you would like to use. Choices are totalgroup, totalotu, averagegroup, averageotu, default is totalgroup.
totalgroup
Abundance / Total number of sequences in the group.
mothur > get.relabund(shared=abrecovery.fn.shared, label=unique-0.03-0.05-0.10, scale=totalgroup)
In the file abrecovery.fn.relabund you would see something like:
unique B 242 0.000000 0.000000 0.000000 0.000000 0.000000 0.011905 ... unique C 242 0.013514 0.013514 0.013514 0.000000 0.013514 0.000000 ... unique A 242 0.000000 0.000000 0.000000 0.011905 0.000000 0.000000 ... 0.03 B 168 0.000000 0.000000 0.000000 0.000000 0.000000 0.011905 ... 0.03 C 168 0.013514 0.013514 0.013514 0.000000 0.013514 0.000000 ... 0.03 A 168 0.000000 0.000000 0.000000 0.011905 0.000000 0.000000 ... 0.05 B 138 0.000000 0.000000 0.000000 0.000000 0.000000 0.013514 ... 0.05 C 138 0.013514 0.013514 0.013514 0.000000 0.013514 0.000000 ... 0.05 A 138 0.000000 0.000000 0.000000 0.011905 0.000000 0.000000 ... 0.10 B 112 0.000000 0.000000 0.000000 0.000000 0.000000 0.011905 ... 0.10 C 112 0.013514 0.013514 0.013514 0.000000 0.013514 0.000000 ... 0.10 A 112 0.000000 0.000000 0.000000 0.011905 0.000000 0.000000 ... ...
totalotu
Abundance / Total number of sequences in the OTU.
mothur > get.relabund(shared=abrecovery.fn.shared, label=unique-0.03-0.05-0.10, scale=totalotu)
In the file abrecovery.fn.relabund you would see something like:
unique B 242 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 ... unique C 242 1.000000 1.000000 1.000000 0.000000 1.000000 0.000000 ... unique A 242 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 ... 0.03 B 168 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 ... 0.03 C 168 1.000000 1.000000 1.000000 0.000000 1.000000 0.000000 ... 0.03 A 168 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 ... 0.05 B 138 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 ... 0.05 C 138 1.000000 1.000000 1.000000 0.000000 1.000000 0.000000 ... 0.05 A 138 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 ... 0.10 B 112 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 ... 0.10 C 112 1.000000 1.000000 1.000000 0.000000 1.000000 0.000000 ... 0.10 A 112 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 ... ...
averagegroup
Abundance / (Total number of sequences in the group / Total number of OTU's).
mothur > get.relabund(shared=abrecovery.fn.shared, label=unique-0.03-0.05-0.10, scale=averagegroup)
In the file abrecovery.fn.relabund you would see something like:
unique B 242 0.000000 0.000000 0.000000 0.000000 0.000000 2.880952 ... unique C 242 3.270270 3.270270 3.270270 0.000000 3.270270 0.000000 ... unique A 242 0.000000 0.000000 0.000000 2.880952 0.000000 0.000000 ... 0.03 B 168 0.000000 0.000000 0.000000 0.000000 0.000000 2.000000 ... 0.03 C 168 2.270270 2.270270 2.270270 0.000000 2.270270 0.000000 ... 0.03 A 168 0.000000 0.000000 0.000000 2.000000 0.000000 0.000000 ... 0.05 B 138 0.000000 0.000000 0.000000 0.000000 0.000000 1.642857 ... 0.05 C 138 1.864865 1.864865 1.864865 0.000000 1.864865 0.000000 ... 0.05 A 138 0.000000 0.000000 0.000000 1.642857 0.000000 0.000000 ... 0.10 B 112 0.000000 0.000000 0.000000 0.000000 0.000000 1.333333 ... 0.10 C 112 1.513514 1.513514 1.513514 0.000000 1.513514 0.000000 ... 0.10 A 112 0.000000 0.000000 0.000000 1.333333 0.000000 0.000000 ... ...
averageotu
Abundance / (Total number of sequences in the OTU / Number of groups).
mothur > get.relabund(shared=abrecovery.fn.shared, label=unique-0.03-0.05-0.10, scale=averageotu)
In the file abrecovery.fn.relabund you would see something like:
unique B 242 0.000000 0.000000 0.000000 0.000000 0.000000 3.000000 ... unique C 242 3.000000 3.000000 3.000000 0.000000 3.000000 0.000000 ... unique A 242 0.000000 0.000000 0.000000 3.000000 0.000000 0.000000 ... 0.03 B 168 0.000000 0.000000 0.000000 0.000000 0.000000 3.000000 ... 0.03 C 168 3.000000 3.000000 3.000000 0.000000 3.000000 0.000000 ... 0.03 A 168 0.000000 0.000000 0.000000 3.000000 0.000000 0.000000 ... 0.05 B 138 0.000000 0.000000 0.000000 0.000000 0.000000 3.000000 ... 0.05 C 138 3.000000 3.000000 3.000000 0.000000 3.000000 0.000000 ... 0.05 A 138 0.000000 0.000000 0.000000 3.000000 0.000000 0.000000 ... 0.10 B 112 0.000000 0.000000 0.000000 0.000000 0.000000 3.000000 ... 0.10 C 112 3.000000 3.000000 3.000000 0.000000 3.000000 0.000000 ... 0.10 A 112 0.000000 0.000000 0.000000 3.000000 0.000000 0.000000 ... ...
label
There may only be a couple of lines in your OTU data that you are interested in finding the relative abundance for. There are two options. You could: (i) manually delete the lines you aren't interested in from your list file; (ii) or use the label option. To use the label option with the get.relabund() command you need to know the labels you are interested in. If you want the relative abundance for the lines labeled unique, 0.03, 0.05 and 0.10 you would enter:
mothur > get.relabund(shared=abrecovery.fn.shared, label=unique-0.03-0.05-0.10)
In the file abrecovery.fn.relabund you would see something like:
unique B 242 0.000000 0.000000 0.000000 0.000000 0.000000 0.011905 ... unique C 242 0.013514 0.013514 0.013514 0.000000 0.013514 0.000000 ... unique A 242 0.000000 0.000000 0.000000 0.011905 0.000000 0.000000 ... 0.03 B 168 0.000000 0.000000 0.000000 0.000000 0.000000 0.011905 ... 0.03 C 168 0.013514 0.013514 0.013514 0.000000 0.013514 0.000000 ... 0.03 A 168 0.000000 0.000000 0.000000 0.011905 0.000000 0.000000 ... 0.05 B 138 0.000000 0.000000 0.000000 0.000000 0.000000 0.013514 ... 0.05 C 138 0.013514 0.013514 0.013514 0.000000 0.013514 0.000000 ... 0.05 A 138 0.000000 0.000000 0.000000 0.011905 0.000000 0.000000 ... 0.10 B 112 0.000000 0.000000 0.000000 0.000000 0.000000 0.011905 ... 0.10 C 112 0.013514 0.013514 0.013514 0.000000 0.013514 0.000000 ... 0.10 A 112 0.000000 0.000000 0.000000 0.011905 0.000000 0.000000 ... ...
groups
If you are only interested in the looking at specific samples you could use the groups option:
mothur > get.relabund(shared=abrecovery.fn.shared, groups=B-C)
