parameters_are_good | R Documentation |
Check input parameters.
parameters_are_good( annot, count_data_A, count_data_B, boot_data_A, boot_data_B, TARGET_COL, PARENT_COL, correction, testmode, scaling, threads, seed, p_thresh, abund_thresh, dprop_thresh, qboot, qbootnum, qrep_thresh, rboot, rrep_thresh, reckless, lean, verbose, use_sums )
annot |
Annotation dataframe. |
count_data_A |
A dataframe of estimated counts. |
count_data_B |
A dataframe of estimated counts. |
boot_data_A |
A list of dataframes, one per sample, each with all the bootstrapped estimates for the sample. |
boot_data_B |
A list of dataframes, one per sample, each with all the bootstrapped estimates for the sample. |
TARGET_COL |
Name of transcript id column in annotation. |
PARENT_COL |
Name of gene id column in annotation. |
correction |
P-value correction method. |
testmode |
Which test to run. |
scaling |
Abundance scaling factor. |
threads |
Number of threads. |
seed |
Seed for random engine. |
p_thresh |
Significance level. |
abund_thresh |
Minimum transcript abundance per sample. |
dprop_thresh |
Minimum change in proportion. |
qboot |
Whether to bootstrap against quantifications. |
qbootnum |
Number of bootstrap iterations. |
qrep_thresh |
Confidence threshold. |
rboot |
Whether to bootstrap against samples. |
rrep_thresh |
Confidence threshold. |
reckless |
whether to ignore detected annotation discrepancies. |
lean |
whether to report descriptive statistics for Dprop and pval. |
verbose |
Verbose status. |
use_sums |
Whether to use sums or means. |
List:
"error"logical
"message"string
"maxboots"Infered rule-of-thumbs number of iterations to do.
"warn"logical
"warningslist of strings
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