README.md

In ed-lau/calcDNSAF: dNSAF calculator

calcDNSAF

Calculates dNSAF.

Installation

You can install the released version of calcDNSAF with:

devtools::install_github("ed-lau/calcDNSAF")

Example

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

ed-lau/calcDNSAF documentation built on Nov. 4, 2019, 11:29 a.m.