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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_table or create_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