Description Usage Arguments Value
Correct the error that the same sample with known molecules can show up at slightly different locations when autoradiographed on multiple gels.
1 2 | correct_batch_effect_by_ref(dat_binned_query, dat_binned_ref,
peak_ind_mat_query, peak_ind_mat_ref, bp, score_thres)
|
dat_binned_query |
The binned data to be compressed or stretched towards the reference |
dat_binned_ref |
The binned data to be aligned to. It is usually arbitrarily chosen or the one least visually warped (could be very subjective). We sugguest in one particular analysis, fix this data to be one specific gel. |
peak_ind_mat_query |
A matrix of values, with the first-column entries that equal |
peak_ind_mat_ref |
Same as |
bp |
The break points that binned the smoothed data into bins. |
score_thres |
The score threshold above or equal to which we call peak candidate bins. |
A list of two elements, the first is the vector of break points at reference
peak locations (large to small; NB:check this), the second is a vector of the same length
as the legnth of reference lane, with each element warped_ind[i]
being the index in the query lane
that corresponds for reference index i
.
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