Bioinformatics Asked on July 11, 2021
With the library lipidr lipidomics data has been normalized using the function normalize_pqn()
, and I need to get the normalized data to perform further statistical analysis without using lipidr library, but I am not able to get that data.
The function normalize_pqn()
code is:
function (data, measure = "Area", exclude = "blank",
log = TRUE)
{
data <- .prenormalize_check(data, measure, exclude)
m <- assay(data, measure)
factor_n <- apply(m/rowMeans(m, na.rm = TRUE), 2, median,
na.rm = TRUE)
normalized_m <- apply(m, 1, function(x) x/factor_n) %>% t()
rownames(normalized_m) <- rownames(m)
assay(data, measure) <- normalized_m
data <- set_normalized(data, measure, TRUE)
return(.log_data(data, measure, log))
}
The object lipidomics experiment object has the following structure:
Formal class 'LipidomicsExperiment' [package "lipidr"] with 5 slots
..@ colData :Formal class 'DFrame' [package "S4Vectors"] with 6 slots
.. .. ..@ rownames : chr [1:10] "S1" "S2" "S3" "S4" ...
.. .. ..@ nrows : int 10
.. .. ..@ listData :List of 2
.. .. .. ..$ Type : chr [1:10] "EXO" "EXO" "EXO" "EXO" ...
.. .. .. ..$ Patient: int [1:10] 1 2 3 4 5 1 2 3 4 5
.. .. ..@ elementType : chr "ANY"
.. .. ..@ elementMetadata: NULL
.. .. ..@ metadata : list()
..@ assays :Formal class 'SimpleAssays' [package "SummarizedExperiment"] with 1 slot
.. .. ..@ data:Formal class 'SimpleList' [package "S4Vectors"] with 4 slots
.. .. .. .. ..@ listData :List of 1
.. .. .. .. .. ..$ Area: num [1:1110, 1:10] 0 10.4 0 11.4 0 ...
.. .. .. .. .. .. ..- attr(*, "dimnames")=List of 2
.. .. .. .. .. .. .. ..$ : chr [1:1110] "1" "2" "3" "4" ...
.. .. .. .. .. .. .. ..$ : chr [1:10] "S1" "S2" "S3" "S4" ...
.. .. .. .. ..@ elementType : chr "ANY"
.. .. .. .. ..@ elementMetadata:Formal class 'DFrame' [package "S4Vectors"] with 6 slots
.. .. .. .. .. .. ..@ rownames : NULL
.. .. .. .. .. .. ..@ nrows : int 1
.. .. .. .. .. .. ..@ listData :List of 2
.. .. .. .. .. .. .. ..$ logged : logi TRUE
.. .. .. .. .. .. .. ..$ normalized: logi TRUE
.. .. .. .. .. .. ..@ elementType : chr "ANY"
.. .. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. .. ..@ metadata : list()
.. .. .. .. ..@ metadata : list()
..@ NAMES : chr [1:1110] "1" "2" "3" "4" ...
..@ elementMetadata:Formal class 'DFrame' [package "S4Vectors"] with 6 slots
.. .. ..@ rownames : NULL
.. .. ..@ nrows : int 1110
.. .. ..@ listData :List of 22
.. .. .. ..$ filename : chr [1:1110] "dataframe" "dataframe" "dataframe" "dataframe" ...
.. .. .. ..$ Molecule : chr [1:1110] "3-Hydroxymethylglutaric acid" "Maltulose" "trans-2-Hexenedioic acid" "L-Histidine" ...
.. .. .. ..$ clean_name : chr [1:1110] "acid 3-Hydroxymethylglutaric" "Maltulose" "trans-2-Hexenedioic acid" "L-Histidine" ...
.. .. .. ..$ ambig : logi [1:1110] FALSE FALSE FALSE FALSE FALSE FALSE ...
.. .. .. ..$ not_matched: logi [1:1110] TRUE TRUE TRUE TRUE TRUE TRUE ...
.. .. .. ..$ istd : logi [1:1110] FALSE FALSE FALSE FALSE FALSE FALSE ...
.. .. .. ..$ class_stub : chr [1:1110] NA NA NA NA ...
.. .. .. ..$ chain1 : chr [1:1110] NA NA NA NA ...
.. .. .. ..$ l_1 : int [1:1110] NA NA NA NA NA NA NA NA NA NA ...
.. .. .. ..$ s_1 : int [1:1110] NA NA NA NA NA NA NA NA NA NA ...
.. .. .. ..$ chain2 : chr [1:1110] NA NA NA NA ...
.. .. .. ..$ l_2 : int [1:1110] NA NA NA NA NA NA NA NA NA NA ...
.. .. .. ..$ s_2 : int [1:1110] NA NA NA NA NA NA NA NA NA NA ...
.. .. .. ..$ chain3 : chr [1:1110] NA NA NA NA ...
.. .. .. ..$ l_3 : int [1:1110] NA NA NA NA NA NA NA NA NA NA ...
.. .. .. ..$ s_3 : int [1:1110] NA NA NA NA NA NA NA NA NA NA ...
.. .. .. ..$ chain4 : chr [1:1110] NA NA NA NA ...
.. .. .. ..$ l_4 : logi [1:1110] NA NA NA NA NA NA ...
.. .. .. ..$ s_4 : logi [1:1110] NA NA NA NA NA NA ...
.. .. .. ..$ total_cl : int [1:1110] NA NA NA NA NA NA NA NA NA NA ...
.. .. .. ..$ total_cs : int [1:1110] NA NA NA NA NA NA NA NA NA NA ...
.. .. .. ..$ Class : chr [1:1110] NA NA NA NA ...
.. .. ..@ elementType : chr "ANY"
.. .. ..@ elementMetadata: NULL
.. .. ..@ metadata : list()
..@ metadata :List of 2
.. ..$ summarized: logi FALSE
.. ..$ dimnames : chr [1:2] "TransitionId" "Sample"
When I use the function assay()
I get the data but not the normalize data.
Thank you in advance!
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