contamination.stats: Contamination filtering.
In imminfo/tcr: Advanced Data Analysis of Immune Receptor Repertoires

Description Usage Arguments Value

Occasionally DNA or RNA libraries are contaminate each other. To address this issue and estimate contamination rate tcR offers contamination.stats and decontamination functions. The decontamination function received data (either data frame or a list with data frames) and a limit for clonal proportion as arguments. Script searches for a similar clones to the first data frame in the other (or performs pairwise searches if the given data is a list) and removes clones from the first data frame, which has been found in the second one with counts less or equal to 10 * counts of similar clones in the first one. Function contamination.stats will return the number of clones which will be removed with the contamination.stats function.

1
2
3

contamination.stats(.data1, .data2, .limit = 20, .col = 'Read.count')

decontamination(.data1, .data2, .limit = 20, .col = 'Read.count', .symm = T)

`.data1`	First data frame with columns 'CDR3.nucleotide.sequence' and 'Read.count'. Will be checked for contamination.
`.data2`	Second data frame with such columns. Will be used for checking for sequences which contaminated the first one.
`.limit`	Parameter for filtering: all sequences from `.data1` which are presented in `.data2` and (count of in `.data2`) / (count of seq in `.data1`) >= `.limit` are removed.
`.col`	Column's name with clonal count.
`.symm`	if T then perform filtering out of sequences in .data1, and then from .data2. Else only from .data1.