createBaseline | R Documentation |
createBaseline
creates and initialize a Baseline
object.
createBaseline(
description = "",
db = data.frame(),
regionDefinition = createRegionDefinition(),
testStatistic = "",
regions = NULL,
numbOfSeqs = matrix(),
binomK = matrix(),
binomN = matrix(),
binomP = matrix(),
pdfs = list(),
stats = data.frame()
)
description |
|
db |
|
regionDefinition |
RegionDefinition object defining the regions and boundaries of the Ig sequences. |
testStatistic |
|
regions |
|
numbOfSeqs |
|
binomK |
|
binomN |
|
binomP |
|
pdfs |
|
stats |
|
Create and initialize a Baseline
object.
The testStatistic
indicates the statistical framework used to test for selection.
For example,
local
= CDR_R / (CDR_R + CDR_S).
focused
= CDR_R / (CDR_R + CDR_S + FWR_S).
immbalance
= CDR_R + CDR_s / (CDR_R + CDR_S + FWR_S + FWR_R)
For focused
the regionDefinition
must only contain two regions. If more
than two regions are defined, then the local
test statistic will be used.
For further information on the frame of these tests see Uduman et al. (2011).
A Baseline
object.
Hershberg U, et al. Improved methods for detecting selection by mutation analysis of Ig V region sequences. Int Immunol. 2008 20(5):683-94.
Uduman M, et al. Detecting selection in immunoglobulin sequences. Nucleic Acids Res. 2011 39(Web Server issue):W499-504.
Yaari G, et al. Models of somatic hypermutation targeting and substitution based on synonymous mutations from high-throughput immunoglobulin sequencing data. Front Immunol. 2013 4(November):358.
See Baseline for the return object.
# Creates an empty Baseline object
createBaseline()
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