Description Usage Arguments Value Examples
Subsetting LATMX2 datasets according to genes, sex and tissues, and filtering out features with too many NAs, too low variance, or too many imputed values (proteomics datasets only)
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 | subsetting(
x,
set.c = NULL,
genes.vc = "all",
sex.vc = "all",
tissues.vc = "all",
common_samples.l = FALSE,
na_thresh.n = 0.2,
var_thresh.n = 1e-05,
imputed_thresh.n = 0.2
)
## S4 method for signature 'MultiDataSet'
subsetting(
x,
set.c = NULL,
genes.vc = "all",
sex.vc = "all",
tissues.vc = "all",
common_samples.l = FALSE,
na_thresh.n = 0.2,
var_thresh.n = 1e-05,
imputed_thresh.n = 0.2
)
## S4 method for signature 'ExpressionSet'
subsetting(
x,
set.c = NULL,
genes.vc = "all",
sex.vc = "all",
tissues.vc = NULL,
common_samples.l = NULL,
na_thresh.n = 0.2,
var_thresh.n = 1e-05,
imputed_thresh.n = 0.2
)
|
x |
An S4 object of class |
set.c |
Character: name of the |
genes.vc |
Character vector: with elements in 'LAT', 'MX2', and 'WT'; when set to 'all', the 'c('WT', 'LAT', 'MX2')' vector will be used |
sex.vc |
Character vector: with elements in 'M' and 'F'; when set to 'all', the 'c('M', 'F')' vector will be used |
tissues.vc |
Character vector: with elements in 'liver' and 'plasma'; when set to 'all', the 'c('liver', 'plasma')' vector will be used |
common_samples.l |
Logical: should the datasets be restricted to common samples? |
na_thresh.n |
Numeric: maximal proportion of NAs for a feature to be kept |
var_thresh.n |
Numteric: minimal variance for a feature to be kept |
imputed_thresh.n |
Numeric: for proteomics datasets, the features with a too high proportion of imputed values in all conditions to be compared will be discarded |
ExpressionSet
or MultiDataSet
with the selected sets, samples,
and features (after filtering for the proportion of NAs, the minimum of variance,
and the proportion of imputed values for proteomics datasets)
1 2 3 4 5 | latmx2.mset <- phenomis::reading(LATMX2::statistics_intraomics_dir.c(),
report.c = "none")
plasma_lat.mset <- ProMetIA::subsetting(latmx2.mset,
genes.vc = c("WT", "LAT"),
tissues.vc = "plasma")
|
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