Percentage of contaminants per sample
Calculates the percentage of contaminating proteins as the share of total intensity
qc_contaminants( data, sample, protein, is_contaminant, intensity, n_contaminants = 5, plot = TRUE, interactive = FALSE )
data |
a data frame containing at least the input variables. |
sample |
the name of the column containing the sample names. |
protein |
the name of the column containing protein IDs or protein names. |
is_contaminant |
the name of the column containing a logical indicating if the protein is a contaminant. |
intensity |
the name of the column containing the corresponding raw or untransformed normalised intensity values. |
n_contaminants |
numeric, indicating how many contaminants should be displayed individually. The rest is combined to a group called "other". The default is 5. |
plot |
logical, if TRUE a plot is returned. If FALSE a table is returned. |
interactive |
logical, if TRUE the plot is interactive using plotly. |
A bar plot that displays the percentage of contaminating proteins over all samples. If plot = FALSE a data frame is returned.
## Not run: qc_contaminants( data, sample = sample, protein = leading_razor_protein, is_contaminant = potential_contaminant, intensity = intensity ) ## End(Not run)
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