View source: R/fct_analysis_random.R
find_contrast_samples | R Documentation |
Find the samples that are in the group of the selected contrast. Can be used to subset the data to only include the samples that correspond to the chosen comparison.
find_contrast_samples(
select_contrast,
all_sample_names,
sample_info = NULL,
select_factors_model = NULL,
select_model_comprions = NULL,
reference_levels = NULL,
counts_deg_method = NULL,
data_file_format = NULL
)
select_contrast |
String designating the comparison from DEG analysis to
filter for the significant genes. See the 'comparison' element from the list
returned from |
all_sample_names |
List of the column names of the processed gene data |
sample_info |
Matrix of experiment design information for grouping samples |
select_factors_model |
List designating the selected factors for the
model expression. Example, c("P53", "Treatment"). See
|
select_model_comprions |
String designating selected comparisons to analyze in the DEG analysis |
reference_levels |
Vector of reference levels to use for the
selected factors. Should be in the form of "p53: NULL vs. WT". See
|
counts_deg_method |
Integer indicating method of DEG analysis being performed. This should be one of 1 for limma-trend, 2 for limma-voom, and 3 for DESeq2. |
data_file_format |
Integer indicating the data format. This should be one of 1 for read counts data, 2 for normalized expression, or 3 for fold changes and adjusted P-values |
A numeric vector that can be used to index the processed data and subset to only include the columns from the selected contrast.
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