Calculates dNSAF.
You can install the released version of calcDNSAF with:
devtools::install_github("ed-lau/calcDNSAF")Example usage using the example data from the package:
library(calcDNSAF)
out <- calcDNSAF::dnsaf(percolatorFile = percolatorFile, fasta = Mm_UniProt, test_run=T, q_cutoff=0.01)#>
#> Attaching package: 'kableExtra'
#> The following object is masked from 'package:dplyr':
#>
#> group_rows
|
Uniprot |
uniqueCounts |
len |
distributedCounts |
SAF |
dSAF |
NSAF |
dNSAF |
|---|---|---|---|---|---|---|---|
|
sp|E9PZQ0|RYR1_MOUSE |
1e+00 |
5.0e+03 |
5.0e-01 |
0e+00 |
0e+00 |
0.0e+00 |
0.0e+00 |
|
sp|E9Q401|RYR2_MOUSE |
1e+00 |
5.0e+03 |
5.0e-01 |
0e+00 |
0e+00 |
0.0e+00 |
0.0e+00 |
|
sp|O08749|DLDH_MOUSE |
2e+00 |
5.1e+02 |
2.0e+00 |
0e+00 |
0e+00 |
2.0e-02 |
2.0e-02 |
|
sp|O55143|AT2A2_MOUSE |
9e+00 |
1.0e+03 |
7.8e+00 |
1e-02 |
1e-02 |
4.0e-02 |
4.0e-02 |
|
sp|O70250|PGAM2_MOUSE |
1e+00 |
2.5e+02 |
1.0e+00 |
0e+00 |
0e+00 |
2.0e-02 |
2.0e-02 |
|
sp|O70468|MYPC3_MOUSE |
2e+00 |
1.3e+03 |
2.0e+00 |
0e+00 |
0e+00 |
1.0e-02 |
1.0e-02 |
|
sp|P02301|H3C_MOUSE |
2e+00 |
1.4e+02 |
1.0e+00 |
1e-02 |
1e-02 |
7.0e-02 |
4.0e-02 |
|
sp|P07724|ALBU_MOUSE |
1e+00 |
6.1e+02 |
1.0e+00 |
0e+00 |
0e+00 |
1.0e-02 |
1.0e-02 |
|
sp|P07759|SPA3K_MOUSE |
1e+00 |
4.2e+02 |
1.0e+00 |
0e+00 |
0e+00 |
1.0e-02 |
1.0e-02 |
|
sp|P09671|SODM_MOUSE |
1e+00 |
2.2e+02 |
1.0e+00 |
0e+00 |
0e+00 |
2.0e-02 |
3.0e-02 |
|
sp|P13707|GPDA_MOUSE |
1e+00 |
3.5e+02 |
1.0e+00 |
0e+00 |
0e+00 |
1.0e-02 |
2.0e-02 |
|
sp|P16858|G3P_MOUSE |
2e+00 |
3.3e+02 |
2.0e+00 |
1e-02 |
1e-02 |
3.0e-02 |
3.0e-02 |
|
sp|P26231|CTNA1_MOUSE |
1e+00 |
9.1e+02 |
1.0e+00 |
0e+00 |
0e+00 |
1.0e-02 |
1.0e-02 |
|
sp|P29699|FETUA_MOUSE |
1e+00 |
3.4e+02 |
1.0e+00 |
0e+00 |
0e+00 |
1.0e-02 |
2.0e-02 |
|
sp|P35486|ODPA_MOUSE |
2e+00 |
3.9e+02 |
2.0e+00 |
1e-02 |
1e-02 |
3.0e-02 |
3.0e-02 |
|
sp|P41216|ACSL1_MOUSE |
1e+00 |
7.0e+02 |
1.0e+00 |
0e+00 |
0e+00 |
1.0e-02 |
1.0e-02 |
|
sp|P45952|ACADM_MOUSE |
1e+00 |
4.2e+02 |
1.0e+00 |
0e+00 |
0e+00 |
1.0e-02 |
1.0e-02 |
|
sp|P50544|ACADV_MOUSE |
2e+00 |
6.6e+02 |
2.0e+00 |
0e+00 |
0e+00 |
1.0e-02 |
2.0e-02 |
|
sp|P52825|CPT2_MOUSE |
1e+00 |
6.6e+02 |
1.0e+00 |
0e+00 |
0e+00 |
1.0e-02 |
1.0e-02 |
|
sp|P54071|IDHP_MOUSE |
1e+00 |
4.5e+02 |
1.0e+00 |
0e+00 |
0e+00 |
1.0e-02 |
1.0e-02 |
|
sp|P56480|ATPB_MOUSE |
5e+00 |
5.3e+02 |
5.0e+00 |
1e-02 |
1e-02 |
5.0e-02 |
5.0e-02 |
|
sp|P62631|EF1A2_MOUSE |
1e+00 |
4.6e+02 |
1.0e+00 |
0e+00 |
0e+00 |
1.0e-02 |
1.0e-02 |
|
sp|P62737|ACTA_MOUSE |
1e+00 |
3.8e+02 |
2.5e-01 |
0e+00 |
0e+00 |
1.0e-02 |
0.0e+00 |
|
sp|P63038|CH60_MOUSE |
3e+00 |
5.7e+02 |
3.0e+00 |
1e-02 |
1e-02 |
3.0e-02 |
3.0e-02 |
|
sp|P63242|IF5A1_MOUSE |
1e+00 |
1.5e+02 |
1.0e+00 |
1e-02 |
1e-02 |
3.0e-02 |
4.0e-02 |
|
sp|P63268|ACTH_MOUSE |
1e+00 |
3.8e+02 |
2.5e-01 |
0e+00 |
0e+00 |
1.0e-02 |
0.0e+00 |
|
sp|P68033|ACTC_MOUSE |
1e+00 |
3.8e+02 |
2.5e-01 |
0e+00 |
0e+00 |
1.0e-02 |
0.0e+00 |
|
sp|P68134|ACTS_MOUSE |
1e+00 |
3.8e+02 |
2.5e-01 |
0e+00 |
0e+00 |
1.0e-02 |
0.0e+00 |
|
sp|P84244|H33_MOUSE |
2e+00 |
1.4e+02 |
1.0e+00 |
1e-02 |
1e-02 |
7.0e-02 |
4.0e-02 |
|
sp|P97807|FUMH_MOUSE |
1e+00 |
5.1e+02 |
1.0e+00 |
0e+00 |
0e+00 |
1.0e-02 |
1.0e-02 |
|
sp|Q02566|MYH6_MOUSE |
8e+00 |
1.9e+03 |
6.7e+00 |
0e+00 |
0e+00 |
2.0e-02 |
2.0e-02 |
|
sp|Q03265|ATPA_MOUSE |
1e+00 |
5.5e+02 |
1.0e+00 |
0e+00 |
0e+00 |
1.0e-02 |
1.0e-02 |
|
sp|Q61425|HCDH_MOUSE |
7e+00 |
3.1e+02 |
7.0e+00 |
2e-02 |
2e-02 |
1.1e-01 |
1.3e-01 |
|
sp|Q6P8J7|KCRS_MOUSE |
1e+00 |
4.2e+02 |
1.0e+00 |
0e+00 |
0e+00 |
1.0e-02 |
1.0e-02 |
|
sp|Q8BMS1|ECHA_MOUSE |
4e+00 |
7.6e+02 |
4.0e+00 |
1e-02 |
1e-02 |
3.0e-02 |
3.0e-02 |
|
sp|Q8BWT1|THIM_MOUSE |
1e+00 |
4.0e+02 |
1.0e+00 |
0e+00 |
0e+00 |
1.0e-02 |
1.0e-02 |
|
sp|Q8CGK3|LONM_MOUSE |
1e+00 |
9.5e+02 |
1.0e+00 |
0e+00 |
0e+00 |
1.0e-02 |
1.0e-02 |
|
sp|Q8K310|MATR3_MOUSE |
1e+00 |
8.5e+02 |
1.0e+00 |
0e+00 |
0e+00 |
1.0e-02 |
1.0e-02 |
|
sp|Q8R429|AT2A1_MOUSE |
4e+00 |
9.9e+02 |
1.2e+00 |
0e+00 |
0e+00 |
2.0e-02 |
1.0e-02 |
|
sp|Q91VD9|NDUS1_MOUSE |
1e+00 |
7.3e+02 |
1.0e+00 |
0e+00 |
0e+00 |
1.0e-02 |
1.0e-02 |
|
sp|Q91Z83|MYH7_MOUSE |
4e+00 |
1.9e+03 |
1.3e+00 |
0e+00 |
0e+00 |
1.0e-02 |
0.0e+00 |
|
sp|Q99JY0|ECHB_MOUSE |
1e+00 |
4.8e+02 |
1.0e+00 |
0e+00 |
0e+00 |
1.0e-02 |
1.0e-02 |
|
sp|Q99KI0|ACON_MOUSE |
4e+00 |
7.8e+02 |
4.0e+00 |
1e-02 |
1e-02 |
3.0e-02 |
3.0e-02 |
|
sp|Q99NB1|ACS2L_MOUSE |
1e+00 |
6.8e+02 |
1.0e+00 |
0e+00 |
0e+00 |
1.0e-02 |
1.0e-02 |
|
sp|Q9CR68|UCRI_MOUSE |
1e+00 |
2.7e+02 |
1.0e+00 |
0e+00 |
0e+00 |
2.0e-02 |
2.0e-02 |
|
sp|Q9CZ13|QCR1_MOUSE |
1e+00 |
4.8e+02 |
1.0e+00 |
0e+00 |
0e+00 |
1.0e-02 |
1.0e-02 |
|
sp|Q9CZU6|CISY_MOUSE |
1e+00 |
4.6e+02 |
1.0e+00 |
0e+00 |
0e+00 |
1.0e-02 |
1.0e-02 |
|
sp|Q9D0F9|PGM1_MOUSE |
1e+00 |
5.6e+02 |
1.0e+00 |
0e+00 |
0e+00 |
1.0e-02 |
1.0e-02 |
|
sp|Q9D0M3|CY1_MOUSE |
2e+00 |
3.2e+02 |
2.0e+00 |
1e-02 |
1e-02 |
3.0e-02 |
3.0e-02 |
|
sp|Q9DCS3|MECR_MOUSE |
1e+00 |
3.7e+02 |
1.0e+00 |
0e+00 |
0e+00 |
1.0e-02 |
2.0e-02 |
|
sp|Q9DCT8|CRIP2_MOUSE |
1e+00 |
2.1e+02 |
1.0e+00 |
0e+00 |
0e+00 |
2.0e-02 |
3.0e-02 |
|
sp|Q9JHI5|IVD_MOUSE |
1e+00 |
4.2e+02 |
1.0e+00 |
0e+00 |
0e+00 |
1.0e-02 |
1.0e-02 |
|
sp|Q9QXX4|CMC2_MOUSE |
1e+00 |
6.8e+02 |
1.0e+00 |
0e+00 |
0e+00 |
1.0e-02 |
1.0e-02 |
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