The phrase "assigned copies" is correct and usable in written English.
It can be used when referring to copies of documents or materials that have been designated or allocated to someone for a specific purpose.
Example: "The teacher distributed the assigned copies of the textbook to each student at the beginning of the semester."
Alternatives: "designated copies" or "allocated copies".
We then partitioned the genome into regions reflecting copy number changes and assigned copy number using two independent classification methods (see Materials and Methods).
In total, there were 2,223 genes assigned copy numbers (Additional file 6: Table S16).
Using these four methods, we assigned copy number values to each probe and each CoLaus individual.
There was substantial variation in the confidence with which integer copy numbers were assigned, with MR ranging from just above unity (i.e., the assigned copy number was only marginally favoured over an alternative) to several million-fold.
However, on chromosome 14, it could be deducted that the assigned copy number state 2 intensity value corresponded to 4 DNA copies (for detailed information, please refer to the figure legend).
qPCR results showed that two of these clones (SoPIP1 2: 1000:2 and SoPIP1 2: 1000:3) carried only one copy of the SoPIP1 2 gene and three of them (SoPIP1 2: 500 1, SoPIP1 2: 2000:1 and SoPIP1 2: 2000:2) were assigned copy numbers close to four.
As in paper [ 27], the log2 ratio is calculated by (1) l o g 2 r a t i o = log 2 (c P t + 2 (1 − P t ) 2 ), where c is the assigned copy number.
P value determined by Chi-square approximation P-value < 0.001 To objectively assess "genomic instability", we calculated a loss/normal/gain value for every gene using the SWITCHdna assigned copy number states, and calculated the levels of genomic instability by subtype using the average number of gains/losses per sample on a gene by gene basis.
On the other hand, Birdsuite packages sequentially assigns copy number genotypes across common CNVs (Canary: uses a Gaussian Mixture Model approach and heuristics to determine the CN genotypes), calls genotypes of SNPs (Birdseed), identifies rare CNVs via a hidden Markov model (HMM) approach (Birdseye) on a sample basis and generates an integrated sequence and CN genotype at each locus (Fawkes).
In general, to simulate a rule-based model, one must assign copy numbers to molecules and rate constants to rate laws.
