summarizeSequenceStatus: Summarize sequence status

In LTLA/RepertoireUtils: Utility Functions for Analyzing Repertoire Sequencing Data

Description

Obtain a quick summary of the status of the sequences for a particular component.

Usage

summarizeSequenceStatus(x, group = NULL)

Arguments

x	A SplitDataFrameList where each DataFrame corresponds to a cell and each row in that DataFrame is a sequence in that cell.
group	Factor of length equal to x indicating the group to which each cell belongs.

Details

By default, this assumes that the fields are named in the same manner as the annotation files produced by CellRanger. Future iterations will provide support for more standardized formats like AIRR.

Value

If group=NULL, a DataFrame is returned with one row per cell, indicating whether that cell has:

• any sequence

• multiple sequences

• any productive sequence

• any full-length sequence

• any high-confidence sequence

• any awesome (productive, full-length and high-confidence) sequence

If group is specified, the DataFrame instead contains one row per level of group. Each value then represents the proportion of cells in that group with any sequence, multiple sequences, etc.

Author(s)

Aaron Lun

See Also

countSequencesPerCell, for which this function is a wrapper.

Examples

df <- data.frame(
    cell.id=sample(LETTERS, 30, replace=TRUE),
    clonotype=sample(paste0("clonotype_", 1:5), 30, replace=TRUE),
    full_length=sample(c("True", "False"), 30, replace=TRUE),
    high_confidence=sample(c("True", "False"), 30, replace=TRUE),
    productive=sample(c("True", "False"), 30, replace=TRUE),
    umi=pmax(1, rpois(30, 5))
)

Y <- splitDataFrameByCell(df, "cell.id")
summarizeSequenceStatus(Y)

summarizeSequenceStatus(Y, group=sample(1:3, nrow(df), replace=TRUE))

LTLA/RepertoireUtils documentation built on Feb. 9, 2020, 12:51 p.m.