Description Usage Arguments Details Value Examples
keep_variable() takes as input a 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> | and returns a 'tbl' with additional columns for the statistics from the hypothesis test.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 | keep_variable(
.data,
.sample = NULL,
.transcript = NULL,
.abundance = NULL,
top = 500,
log_transform = TRUE
)
## S4 method for signature 'spec_tbl_df'
keep_variable(
.data,
.sample = NULL,
.transcript = NULL,
.abundance = NULL,
top = 500,
log_transform = TRUE
)
## S4 method for signature 'tbl_df'
keep_variable(
.data,
.sample = NULL,
.transcript = NULL,
.abundance = NULL,
top = 500,
log_transform = TRUE
)
## S4 method for signature 'tidybulk'
keep_variable(
.data,
.sample = NULL,
.transcript = NULL,
.abundance = NULL,
top = 500,
log_transform = TRUE
)
## S4 method for signature 'SummarizedExperiment'
keep_variable(
.data,
.sample = NULL,
.transcript = NULL,
.abundance = NULL,
top = 500,
log_transform = TRUE
)
## S4 method for signature 'RangedSummarizedExperiment'
keep_variable(
.data,
.sample = NULL,
.transcript = NULL,
.abundance = NULL,
top = 500,
log_transform = TRUE
)
|
.data |
A 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> | |
.sample |
The name of the sample column |
.transcript |
The name of the transcript/gene column |
.abundance |
The name of the transcript/gene abundance column |
top |
Integer. Number of top transcript to consider |
log_transform |
A boolean, whether the value should be log-transformed (e.g., TRUE for RNA sequencing data) |
maturing
At the moment this function uses edgeR https://doi.org/10.1093/bioinformatics/btp616
A 'tbl' with additional columns for the statistics from the hypothesis test (e.g., log fold change, p-value and false discovery rate).
Underlying method: s <- rowMeans((x - rowMeans(x)) ^ 2) o <- order(s, decreasing = TRUE) x <- x[o[1L:top], , drop = FALSE] variable_trancripts = rownames(x)
A 'tbl' with additional columns for the statistics from the hypothesis test (e.g., log fold change, p-value and false discovery rate).
A 'tbl' with additional columns for the statistics from the hypothesis test (e.g., log fold change, p-value and false discovery rate).
A 'tbl' with additional columns for the statistics from the hypothesis test (e.g., log fold change, p-value and false discovery rate).
A 'SummarizedExperiment' object
A 'SummarizedExperiment' object
1 2 3 4 5 6 7 | keep_variable(
tidybulk::counts_mini,
sample,
transcript,
`count`,
top = 500
)
|
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