get_csc calculate codon occurrence to mRNA stability correlation coefficients (Default to Pearson's).
Usage
est_csc(
seqs,
half_life,
codon_table = get_codon_table(),
cor_method = "pearson"
)Arguments
- seqs
CDS sequences of all protein-coding genes. One for each gene.
- half_life
data.frame of mRNA half life (gene_id & half_life are column names).
- codon_table
a table of genetic code derived from
get_codon_tableorcreate_codon_table.- cor_method
method name passed to `cor.test` used for calculating correlation coefficients.
Value
a data.table of codons and their CSCs. The columns include codon, codon stability coefficient, and correlation P-value.
References
Presnyak V, Alhusaini N, Chen YH, Martin S, Morris N, Kline N, Olson S, Weinberg D, Baker KE, Graveley BR, et al. 2015. Codon optimality is a major determinant of mRNA stability. Cell 160:1111-1124.
Examples
# estimate yeast mRNA CSC
est_csc(yeast_cds, yeast_half_life)
#> codon csc pvalue
#> <char> <num> <num>
#> 1: TTT -0.0787283632 8.875234e-07
#> 2: TTC 0.0936332740 4.934393e-09
#> 3: TTA -0.0376998334 1.873266e-02
#> 4: TTG 0.1988622236 5.724661e-36
#> 5: TCT 0.1417985154 6.463819e-19
#> 6: TCC 0.1348394407 3.076104e-17
#> 7: TCA -0.1159288994 4.144862e-13
#> 8: TCG -0.1263538419 2.619266e-15
#> 9: TAT -0.0881160809 3.727148e-08
#> 10: TAC 0.0992062077 5.675264e-10
#> 11: TGT -0.0327802019 4.096707e-02
#> 12: TGC -0.0808426979 4.476432e-07
#> 13: TGG -0.0222377555 1.656447e-01
#> 14: CTT -0.1291276840 6.325694e-16
#> 15: CTC -0.1361863222 1.479116e-17
#> 16: CTA -0.1294744450 5.284708e-16
#> 17: CTG -0.1643147443 6.185476e-25
#> 18: CCT 0.0002650952 9.868160e-01
#> 19: CCC -0.0880401578 3.829159e-08
#> 20: CCA 0.1558224407 1.473949e-22
#> 21: CCG -0.1804587973 8.134753e-30
#> 22: CAT -0.0865936247 6.377939e-08
#> 23: CAC 0.0680092776 2.193847e-05
#> 24: CAA 0.0718391124 7.332632e-06
#> 25: CAG -0.1305086656 3.082292e-16
#> 26: CGT 0.0791013333 7.875633e-07
#> 27: CGC -0.1015374063 2.215377e-10
#> 28: CGA -0.1966457587 3.407156e-35
#> 29: CGG -0.1272088127 1.695961e-15
#> 30: ATT 0.0480969867 2.701542e-03
#> 31: ATC 0.1117000075 2.857699e-12
#> 32: ATA -0.2568927250 1.217191e-59
#> 33: ATG -0.0644903332 5.718986e-05
#> 34: ACT 0.1431269860 3.023536e-19
#> 35: ACC 0.1264144565 2.540030e-15
#> 36: ACA -0.1426175629 4.049665e-19
#> 37: ACG -0.1552369990 2.125992e-22
#> 38: AAT -0.1285588646 8.486818e-16
#> 39: AAC 0.0673723086 2.618359e-05
#> 40: AAA -0.1497286397 6.225878e-21
#> 41: AAG 0.1022785721 1.635387e-10
#> 42: AGT -0.1552420723 2.119267e-22
#> 43: AGC -0.1489732334 9.797090e-21
#> 44: AGA 0.0412850037 1.003712e-02
#> 45: AGG -0.1932809538 4.905373e-34
#> 46: GTT 0.1904668721 4.395850e-33
#> 47: GTC 0.1990981824 4.728645e-36
#> 48: GTA -0.1895276774 9.069717e-33
#> 49: GTG -0.0955719036 2.357610e-09
#> 50: GCT 0.2488397109 5.896098e-56
#> 51: GCC 0.1754110472 3.075101e-28
#> 52: GCA -0.0849723268 1.119066e-07
#> 53: GCG -0.1019375045 1.881052e-10
#> 54: GAT -0.0544183892 6.872410e-04
#> 55: GAC 0.0603621379 1.658610e-04
#> 56: GAA 0.0903827731 1.647429e-08
#> 57: GAG -0.1193680732 8.181022e-14
#> 58: GGT 0.2131801918 3.377969e-41
#> 59: GGC -0.0116004256 4.696045e-01
#> 60: GGA -0.1229495155 1.435996e-14
#> 61: GGG -0.0934788330 5.230147e-09
#> codon csc pvalue