View source: R/BioTIP_update_04202022.R
sd_selection | R Documentation |
sd_selection
pre-selects highly oscillating transcripts
from the input dataset df
. The dataset must contain multiple sample
groups (or 'states'). For each state, the function filters the dataset using
a cutoff value for standard deviation. The default cutoff value is 0.01
(i.e., higher than the top 1 percentage standard deviation).
sd_selection(
df,
samplesL,
cutoff = 0.01,
method = c("other", "reference", "previous", "itself", "longitudinal reference"),
control_df = NULL,
control_samplesL = NULL
)
df |
A numeric matrix or data frame. The rows and columns represent unique transcript IDs (geneID) and sample names, respectively. |
samplesL |
A list of vectors, whose length is the number of states. Each vector gives the sample names in a state. Note that the vectors (sample names) has to be among the column names of the R object 'df'. |
cutoff |
A positive numeric value. Default is 0.01. If < 1,
automatically selects top x transcripts using the a selecting
method (which is either the |
method |
Selection of methods from
|
control_df |
A count matrix with unique loci as row names and samples names
of control samples as column names, only used for method |
control_samplesL |
A list of characters with stages as names of control samples, required for method 'longitudinal reference' |
sd_selection()
A list of data frames, whose length is the number
of states. The rows in each data frame are the filtered transcripts with
highest standard deviation selected from df
and based on an assigned cutoff
value. Each resulting data frame represents a subset of the raw
input df
, with the sample ID of the same state in the column.
Zhezhen Wang zhezhen@uchicago.edu
optimize.sd_selection
counts = matrix(sample(1:100, 18), 2, 9)
colnames(counts) = 1:9
row.names(counts) = c('loci1', 'loci2')
cli = cbind(1:9, rep(c('state1', 'state2', 'state3'), each = 3))
colnames(cli) = c('samples', 'group')
samplesL <- split(cli[, 1], f = cli[, 'group'])
test_sd_selection <- sd_selection(counts, samplesL, 0.01)
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