test.li.recstat: Tests if regions located between Stop codons contain putative CDSs.

Description

This test uses rows (windows) factor scores computed by recstat in order to determine if the regions located between two Stop codons correspond to putative CDSs.

Usage

test.li.recstat(rec, fac = 1, length.min = 150, stop.max = 0.2,
    direct = TRUE, level = 0.05)

Arguments

rec

list of elements returned by recstat function.

fac

axis of the CA to use for test (4 \(\ge\) fac \(\ge\) 1).

length.min

minimal length between two Stop codons.

stop.max

threshold for Stop codons relative position in a window to determine if this window can be used for test computation.

direct

a logical for the choice of direct or reverse strand.

level

p-value threshold for t-test.

Value

The result is returned as a list containing three matrices (one for each reading frame). All matrices have the same structure, with rows corresponding to the regions between two Stop codons. Columns Start and End give the location of starting and ending positions of the region; Mean i gives the mean of the factor scores for the windows located in the region, this for reading frame i; t(i,j) gives the p-value of the t-test computed between the means from reading frames i and j; and CDS is a binary indicator equal to 1 if a putative CDS is predicted, and to 0 if not.

Details

The test is computed for all regions between two Stop codons separated by at least length.min nucleotides, this for the three possible reading frames of a DNA strand. For each region considered, two t-tests are computed for comparing the mean of the factor scores of the windows from the reading frame in which the region is located with the means of the factor scores from the corresponding windows in the two other reading frames. If both t-tests reject the null hypothesis of means equality, then there is a good probability that a CDS is located in the region.

Inside the first and the last windows of a region submitted to the test, the relative position of the two Stop codons is used to determine if those windows can be used in the analysis. If the first Stop is located within the stop.max fraction of the 5' end of the window, then this window is kept in the analysis. In the same way, if the second Stop is located within the stop.max fraction of the 3' end of the window, this window is also kept in the analysis.

Examples

Run this code

# NOT RUN {
ff <- system.file("sequences/ECOUNC.fsa", package = "seqinr")
seq <- read.fasta(ff)
rec <- recstat(seq[[1]], seqname = getName(seq))
test.li.recstat(rec)
# }