.read_somascan {autonomics} | R Documentation |
Read data from somascan adat file
.read_somascan( file, fidvar = "SeqId", sidvar = "SampleId", sfile = NULL, sfileby = NULL, by = NULL, subgroupvar = "SampleGroup" ) read_somascan( file, fidvar = "SeqId", sidvar = "SampleId", sfile = NULL, sfileby = NULL, by = NULL, subgroupvar = "SampleGroup", fname_var = "EntrezGeneSymbol", sample_type = "Sample", feature_type = "Protein", sample_quality = c("FLAG", "PASS"), feature_quality = c("FLAG", "PASS"), rm_na_svars = FALSE, rm_single_value_svars = FALSE, pca = FALSE, fit = NULL, formula = NULL, block = NULL, contrastdefs = NULL, verbose = TRUE, plot = TRUE )
file |
*.adat file path (string) |
fidvar |
featureid fvar (string) |
sidvar |
sampleid svar (string) |
sfile |
sample file |
sfileby |
sample file mergeby column |
by |
metabolon file mergeby column |
subgroupvar |
subgroup svar (string) |
fname_var |
featurename fvar (string) |
sample_type |
subset of c('Sample','QC','Buffer','Calibrator') |
feature_type |
subset of c('Protein', 'Hybridization Control Elution', 'Rat Protein') |
sample_quality |
subset of c('PASS', 'FLAG', 'FAIL') |
feature_quality |
subset of c('PASS', 'FLAG', 'FAIL') |
rm_na_svars |
whether to rm NA svars |
rm_single_value_svars |
whether to rm single value svars |
pca |
whether to pca |
fit |
fit model: NULL, 'limma', 'lm', 'lme', 'lmer','wilcoxon' |
formula |
design formula (using svars) |
block |
block var |
contrastdefs |
contrastdef vector/matrix/list |
verbose |
whether to msg |
plot |
whether to plot |
Summarizedexperiment
file <- download_data('atkin18.somascan.adat') read_somascan(file, pca = TRUE, fit = 'limma', block = 'Subject_ID')