In ilangurudev/approxmapR: ApproxMAP (APPROXimate Multiple Alignment Pattern)

knitr::opts_chunk$set(echo = FALSE)

Meta Information

Algorithms being compared are r formatted1_pars$algo and r formatted2_pars$algo. The parameters set for each algorithm are as follows:

• r formatted1_pars$algo: k = r formatted1_pars$k with the r formatted1_pars$pattern filter pattern being used at the threshold of r formatted1_pars$threshold * 100%.
• r formatted2_pars$algo: k = r formatted2_pars$k with the r formatted2_pars$pattern filter pattern being used at the threshold of r formatted2_pars$threshold * 100%.

Comparison

The r formatted1_pars$algo identified r dim(params$formatted1)[1] clusters while the r formatted2_pars$algo algorithm partitioned the data into the set r params$formatted2_pars$k clusters. The largest r formatted1_pars$algo cluster had r params$formatted1$n[[1]] sequences which represents r params$formatted1$n_percent[[1]] of all sequences within the data with the resulting r params$formatted1_pars$pattern being r params$formatted1[1, c(4)]. The largest r formatted2_pars$algo cluster had r params$formatted2$n[[1]] sequences which represents r params$formatted2$n_percent[[1]] of all sequences within the data with the resulting r params$formatted2_pars$pattern being r params$formatted2[1, c(4)].

Running the approxmapR algorithm on the consensus patterns produced by both algorithms using the following parameters:

• r formatted3_pars$algo: k = r formatted3_pars$k with the r formatted3_pars$pattern filter pattern being used at the threshold of r formatted3_pars$threshold * 100%

Resulted in the following:

#::kable(formatted3[, c(1,2,3,4)])
formatted3[, c(1,2,3,4)]

All exported files for the r formatted1_pars$algo and r formatted2_pars$algo, as well as for the comparison can be found r params$approxmapR_results.

ilangurudev/approxmapR documentation built on March 22, 2022, 1:15 p.m.