umiGroup: Group equivalent UMIs
In florian0512/SarlaccSeq: Pipeline for Oxford Nanopore RNA-Seq Data Analysis

Description Usage Arguments Details Value See Also Examples

Identify reads originating from the same DNA molecule, based on similar sequences for the unique molecular identifiers (UMIs).

1 2	umiGroup(UMI1, threshold1=3, UMI2=NULL, threshold2=threshold1, max.err=NA, groups=NULL)

`UMI1`	A DNAStringSet or QualityScaledDNAStringSet object containing the UMI sequence for each read.
`threshold1`	A integer scalar specifying the maximum distance between the UMI sequences of two reads in order for them to be considered equivalent.
`UMI2`	An optional DNAStringSet or QualityScaledDNAStringSet object containing the second UMI sequence for each read.
`threshold2`	A integer scalar specifying the maximum distance between the UMI sequences of two reads in order for them to be considered equivalent.
`max.err`	A numeric scalar specifying the maximum error probability above which bases are to be masked.
`groups`	A factor specifying the group to which each read belongs.

This function will identify groups of reads originating from the same DNA molecule, based on the presence of similar UMI sequences. Each read is represented by a UMI sequence in UMI1, obtained from the read sequence using adaptorAlign.

We use a greedy approach to group reads from the same molecule. For each UMI, we define neighboring UMIs as those within a Levenshtein distance of threshold1. The first group is defined as all neighbors of the UMI with the most neighbors. The process is then repeated with the remaining UMIs. This is a conservative procedure that errs on the side of under-merging to avoid grouping reads from distinct molecules.

Bases with error probabilities above max.err will be masked and replaced with Ns, which contribute 0.5 mismatches to the distance calculation. If UMI2 is supplied, we assume that each read is represented by two UMI sequences (e.g., on both ends of the read). Sequences in UMI1 are compared to other sequences in UMI1, and sequences in UMI2 are compared to other sequences in UMI2. UMIs are only defined as neighbors if the Levenshtein distances for the first and second UMIs are below threshold1 and threshold2, respectively.

If groups is specified, reads are only grouped together if they have the same level of groups. This is useful for restricting the UMI comparisons to pre-defined groups of reads, e.g., reads that map to the same transcript family.

A list of integer vectors, where each vector represents a group and contains the indices of the reads (i.e., with respect to UMI1) in that group.

adaptorAlign to obtain the UMI sequences.

umi1 <- DNAStringSet(c("AACCGGTT", "AACGGTT", 
    "ACCCGGTT", "AACCGGTTT"))

umiGroup(umi1)
umiGroup(umi1, threshold1=0)
   
# Now with qualities.
umiX <- QualityScaledDNAStringSet(umi1, 
    PhredQuality(c("11223344", "1123344", "12223344", "112233444")))
umiGroup(umiX, max.err=0.02)
umiGroup(umiX, max.err=0.02, threshold1=1)

# Now with a UMI2.
umi2 <- DNAStringSet(c("AACCGGTT", "CACCGGTT", 
    "AACCCGGTA", "AACGGGTT"))
umiGroup(umi1, UMI2=umi2)
umiGroup(umi1, UMI2=umi2, threshold2=0)