summarizeBaseline - Calculate BASELINe summary statistics

Description

summarizeBaseline calculates BASELINe statistics such as the mean selection strength (mean Sigma), the 95% confidence intervals and p-values for the presence of selection.

Usage

summarizeBaseline(baseline, returnType = c("baseline", "df"), nproc = 1)

Arguments

baseline
Baseline object returned by calcBaseline containing annotations and BASELINe posterior probability density functions (PDFs) for each sequence.
returnType
One of c("baseline", "df") defining whether to return a Baseline object (“baseline”) with an updated stats slot or a data.frame (“df”) of summary statistics.
nproc
number of cores to distribute the operation over. If nproc = 0 then the cluster has already been set and will not be reset.

Value

Either a modified Baseline object or data.frame containing the mean BASELINe selection strength, its 95% confidence intervals, and a p-value for the presence of selection.

Details

The returned p-value can be either positive or negative. Its magnitude (without the sign) should be interpreted as per normal. Its sign indicates the direction of the selection detected. A positive p-value indicates positive selection, whereas a negative p-value indicates negative selection.

References

  1. Uduman M, et al. Detecting selection in immunoglobulin sequences. Nucleic Acids Res. 2011 39(Web Server issue):W499-504.

Examples

# Subset example data
data(ExampleDb, package="alakazam")
db <- subset(ExampleDb, ISOTYPE %in% c("IgA", "IgG") & SAMPLE == "+7d")

# Calculate BASELINe
baseline <- calcBaseline(db, 
sequenceColumn="SEQUENCE_IMGT",
germlineColumn="GERMLINE_IMGT_D_MASK", 
testStatistic="focused",
regionDefinition=IMGT_V,
targetingModel=HH_S5F,
nproc = 1)

Collapsing clonal sequences...
Calculating the expected frequencies of mutations...
Calculating BASELINe probability density functions...


# Grouping the PDFs by the sample and isotype annotations
grouped <- groupBaseline(baseline, groupBy=c("SAMPLE", "ISOTYPE"))

Grouping BASELINe probability density functions...
Calculating BASELINe statistics...


# Get a data.frame of the summary statistics
stats <- summarizeBaseline(grouped, returnType="df")
Calculating BASELINe statistics...

See also

See calcBaseline for generating Baseline objects and groupBaseline for convolving groups of BASELINe PDFs.