View source: R/tidyMS_aggregation.R
aggregate_intensity_topN | R Documentation |
run rank_peptide_by_intensity first
aggregate_intensity_topN(pdata, config, .func, N = 3)
pdata |
data.frame |
config |
AnalysisConfiguration |
N |
default 3 top intensities. |
func |
function to use for aggregation |
list with data and new reduced configuration (config)
Other aggregation:
INTERNAL_FUNCTIONS_BY_FAMILY
,
estimate_intensity()
,
intensity_summary_by_hkeys()
,
medpolish_estimate()
,
medpolish_estimate_df()
,
medpolish_estimate_dfconfig()
,
medpolish_protein_estimates()
,
plot_estimate()
,
plot_hierarchies_add_quantline()
,
plot_hierarchies_line()
,
plot_hierarchies_line_df()
,
rlm_estimate()
,
rlm_estimate_dfconfig()
dd <- prolfqua::sim_lfq_data_peptide_config()
config <- dd$config
res <- dd$data
ranked <- rank_peptide_by_intensity(res,config)
mean_f <- function(x, name = FALSE){
if(name){return("mean")};mean(x, na.rm=TRUE)
}
sum_f <- function(x, name =FALSE){
if(name){return("sum")};sum(x, na.rm = TRUE)
}
resTOPN <- aggregate_intensity_topN(
ranked,
config,
.func = mean_f,
N=3)
print(dim(resTOPN$data))
# stopifnot(dim(resTOPN$data) == c(3260, 8))
stopifnot( names(resTOPN) %in% c("data", "config") )
config$table$get_response()
#debug(plot_estimate)
tmpRob <- plot_estimate(ranked,
config,
resTOPN$data,
resTOPN$config,
show.legend=TRUE)
stopifnot( "ggplot" %in% class(tmpRob$plots[[4]]) )
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