createSqMass: Create an sqMass file

In Roestlab/DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

Description

Writes a sqMass file having chromatograms and their native IDs.

Usage

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, [e-mail]

ORCID: 0000-0003-3500-8152

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

See Also

createMZML, blobXICs

Examples

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.