createSqMass: Create an sqMass file

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/sqMass.R

Description

Writes a sqMass file having chromatograms and their native IDs.

Usage

1
createSqMass(filename, XICs, transitionIDs, lossy)

Arguments

filename

(string) name of the mzML file to be written. Extension should be .chrom.sqMass.

XICs

(list of list of data-frames) list of extracted ion chromatograms of all precursors.

transitionIDs

(list of integer) length must be the same as of XICs.

lossy

(logical) if TRUE, time and intensity are lossy-compressed.

Details

- compression is one of 0 = no, 1 = zlib, 2 = np-linear, 3 = np-slof, 4 = np-pic, 5 = np-linear + zlib, 6 = np-slof + zlib, 7 = np-pic + zlib
- data_type is one of 0 = mz, 1 = int, 2 = rt
- data contains the raw (blob) data for a single data array

Value

(None)

Author(s)

Shubham Gupta, shubh.gupta@mail.utoronto.ca

ORCID: 0000-0003-3500-8152

License: (c) Author (2021) + GPL-3 Date: 2021-01-16

See Also

createMZML, blobXICs

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
data(XIC_QFNNTDIVLLEDFQK_3_DIAlignR)
XICs <- XIC_QFNNTDIVLLEDFQK_3_DIAlignR[["hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"]]
XICs <- list(XICs[[1]], XICs[[1]])
nativeIds <- list(27706:27711, 1:6)
sqName <- "testfile.chrom.sqMass"
## Not run: 
createSqMass(sqName, XICs, nativeIds, TRUE)
con <- DBI::dbConnect(RSQLite::SQLite(), dbname = sqName)
XIC_group <- extractXIC_group2(con, 0:5)
DBI::dbDisconnect(con)
file.remove(sqName)

## End(Not run)

Roestlab/DIAlignR documentation built on March 3, 2021, 9:09 a.m.