baseline: Pick Baseline Timepoint Samples
In microbiome/microbiome: Microbiome Analytics
baseline R Documentation
Pick Baseline Timepoint Samples
Description
Identify and select the baseline timepoint samples in a
phyloseq object.
Usage
baseline(x, na.omit = TRUE)
Arguments
x
phyloseq object. Assuming that the sample_data(x) has the fields
'time', 'sample' and 'subject'
na.omit
Logical. Ignore samples with no time point information.
If this is FALSE, the first sample for each subject is selected even
when there is no time information.
Details
Arranges the samples by time and picks the first sample for each
subject. Compared to simple subsetting at time point zero, this checks
NAs and possibility for multiple samples at the baseline, and guarantees
that a single sample per subject is selected.
Value
Phyloseq object with only baseline time point samples selected.
Author(s)
Contact: Leo Lahti microbiome-admin@googlegroups.com
References
See citation('microbiome')
Examples
data(peerj32)
a <- baseline(peerj32$phyloseq)
microbiome/microbiome documentation built on Aug. 22, 2023, 7:12 a.m.
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| baseline | R Documentation |
Pick Baseline Timepoint Samples
Description
Identify and select the baseline timepoint samples in a
phyloseq object.
Usage
baseline(x, na.omit = TRUE)
Arguments
x |
phyloseq object. Assuming that the sample_data(x) has the fields 'time', 'sample' and 'subject' |
na.omit |
Logical. Ignore samples with no time point information. If this is FALSE, the first sample for each subject is selected even when there is no time information. |
Details
Arranges the samples by time and picks the first sample for each subject. Compared to simple subsetting at time point zero, this checks NAs and possibility for multiple samples at the baseline, and guarantees that a single sample per subject is selected.
Value
Phyloseq object with only baseline time point samples selected.
Author(s)
Contact: Leo Lahti microbiome-admin@googlegroups.com
References
See citation('microbiome')
Examples
data(peerj32)
a <- baseline(peerj32$phyloseq)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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