met.read_data | R Documentation |
met.read_data
is a wrapper function that constructs an mSet object, adds data from a table file or R dataframe object, applies unspecific and user-defined data filters, and imputes missing values.
met.read_data(
data,
data.type = "conc",
anal.type = "stat",
paired = FALSE,
csvsep = ";",
dec = ".",
sheet = 1,
data.format = "rowu",
lbl.type = "disc",
filt.feat = c(""),
filt.smpl = c(""),
filt.grp = c(""),
filt.method = "none",
remain.num = NULL,
qcFilter = "F",
qc.rsd = 25,
all.rsd = NULL,
imp.method = "lod",
export = FALSE,
img.format = "pdf",
dpi = dpi
)
data |
Enter name of an R dataframe object or the "path name" (in quotes) of the CSV/TSV/XLS/XLSX/TXT file to read. |
data.type |
(Character) The type of data, either "list" (Compound lists), |
anal.type |
(Character) Indicate the analysis module to be performed: |
paired |
(Logical) Indicate if the data is paired ( |
csvsep |
(Character) Enter the separator used in the CSV file (only applicable if reading a ".csv" file). |
dec |
(Character) decimal separator used in CSV, TSV and TXT files. |
sheet |
(Integer or Character string) Number or name of the sheet with proteomics data in XLS or XLSX files (optional). |
data.format |
(Character) Specify if samples are paired and in rows ( |
lbl.type |
(Character) Specify the group label type, either categorical ( |
filt.feat |
(Character Vector) Enter the names of features to remove from the dataset. |
filt.smpl |
(Character Vector) Enter the names of samples to remove from the dataset. |
filt.grp |
(Character Vector) Enter the names of groups to remove from the dataset. |
filt.method |
(Character) Select an option for unspecific filtering based on the following ranking criteria:
|
remain.num |
(Numerical) Enter the number of variables to keep in your dataset. If
|
qcFilter |
(Logical) Filter the variables based on the relative standard deviation of features in quality control (QC) samples ( |
qc.rsd |
(Numeric) Define the relative standard deviation cut-off in %. Variables with a RSD greater than this number in the QC samples will be removed from the dataset. It is only necessary to specify this argument if |
all.rsd |
(Numeric or |
imp.method |
(Character) Select the option to replace missing variables:
|
export |
(Logical, |
img.format |
(Character, |
dpi |
(Numeric) The resolution of exported PNG and PDF images. |
An mSet object with (built in ascending order):
original data at mSetObj$dataSet$data_orig
.
data with manually filtered out features/samples/groups at mSetObj$dataSet$edit
.
data with unspecifically filtered data at mSetObj$dataSet$filt
.
data with imputed missing values at mSetObj$dataSet$data_proc
.
missing value heatmap at mSetObj$imgSet$missval_heatmap.plot
(see met.plot_missval
).
Density and CumSum plots of intensities of proteins with and without missing values at mSetObj$imgSet$missval_density.plot
(see met.plot_detect
).
Nicolas T. Wirth mail.nicowirth@gmail.com Technical University of Denmark License: GNU GPL (>= 2)
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