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We randomly permute g i 's expression and compute the nominal p-value for the linkage between the random expression and a locus in the list and retain the smallest p-value.
For each gene g i in a selected locus gene pair from step (v), we maintain a locus list (l j 1, l j 2,…, l jd ), where each locus in the list appears with g i in one of selected locus gene pairs.
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Each locus combination in the list is then depicted on the GM of the marker, as explained above.
The number of loci contained in the list of the NEIS locus identifiers is not static and will change as loci are curated and added to the database over time.
Instead, the loci in this list have FST outside the bootstrap confidence limits [ 34] for both data sets.
For each locus, any position included in any transcript deriving from that locus was included in the list of exonic positions for that gene.
407,465 (~96%) of these chip loci were present in the list of variants identified by sequencing, and over 93% of the loci showed agreement (Table 1).
The result showed that most of the DM loci in these lists were overlapped with M-L DM loci list and at least 98.2% of the overlapped DM loci had the same alteration states (binomial test, all P-value <2.2 × 10−16; Supplementary Table S1).
The alteration states of DM loci in the two lists are considered significantly consistent if the binomial P-value is smaller than 0.05.
For example, the number of hypermethylated loci (n = 479) in the list represent only 1.8% of the total autosomal loci (n = 26486).
Increasing our stringency thresholds for SNPs in the WGS decreased the number chip loci that were present in the list of SNPs identified by sequencing (n = 329,690; ~78%), but increased concordance to ~95%.
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