prot.read_data | R Documentation |
prot.read_data
takes a table file containing proteomics data and filters proteins based on missing values (see prot.filter_missing
) or a given relative standard deviation threshold, and creates a SummarizedExperiment
object.
prot.read_data(
data = "dat_prot.csv",
expdesign = NULL,
csvsep = ";",
dec = ".",
na.strings = "",
sheet = 1,
filter = c("Reverse", "Potential contaminant"),
rsd_thresh = NULL,
name = "Gene Symbol",
id = "Ensembl Gene ID",
pfx = "abundances.",
filt_type = c("condition", "complete", "fraction", NULL),
filt_thr = 3,
filt_min = NULL,
log2_transform = TRUE
)
data |
An R dataframe object or a table file with extension '.xlsx', '.xls', '.csv', '.tsv', or '.txt' containing proteomics data. The table must contain:
|
expdesign |
(optional, if made previously) An R dataframe object or a table file containing the columns 'label', 'condition', and 'replicate' with label = "condition_replicate". If |
csvsep |
(Character string) separator used in CSV files (ignored for other file types). Default: |
dec |
(Character string) decimal separator used in CSV, TSV or TXT files (ignored for other file types). Default: |
na.strings |
A character vector of strings which are to be interpreted as NA values. |
sheet |
(Integer or Character string) Number or name of the sheet with proteomics data in XLS or XLSX files (optional). |
filter |
(Character string or vector of strings) Provide the header of a column containing "+" or "-" to indicate if proteins should be discarded or kept, respectively. |
rsd_thresh |
(Numeric, optional) Provide a relative standard deviation (RSD) threshold in % for proteins. The RSD is calculated for each condition and if the maximum RSD value determined for a given protein exceeds |
name |
(Character string) Provide the header of the column containing protein names. |
id |
(Character string) Provide the header of the column containing protein IDs |
pfx |
(Character string) Provide the common prefix for headers containing abundance values (e.g., "abundances."). |
filt_type |
(Character string) "complete", "condition" or "fraction", Sets the type of filtering applied. "complete" will only keep proteins with valid values in all samples. "condition" will keep proteins that have a maximum of |
filt_thr |
(Integer) Sets the threshold for the allowed number of missing values in at least one condition if |
filt_min |
(Numeric) Sets the threshold for the minimum fraction of valid values allowed for any protein if |
log2_transform |
(Logical) Should the data be log2 transformed? |
A filtered SummarizedExperiment object.
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