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.
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