MetaboAnalystR (version 2.0.0)

SetPeakParam: Set parameters for peak picking using XCMS and CAMERA

Description

This function sets all the parameters used for downstream pre-processing of user's raw MS data.

Usage

SetPeakParam(alg = "centwave", ppm = 10, min_pkw = 10,
  max_pkw = 60, sn_thresh = 6, mzdiff = 0.01, bw = 5,
  min_frac = 0.5, min_sample_num = 1, max_feats = 100,
  bin_size = 1, rt_filt = FALSE, rt_min = 200, rt_max = 1000)

Arguments

alg

Character, specify the algorithm to perform peak detection. "centwave" to use the CentWave algorithm, and "match_filt" to use the MatchedFilter algorithm.

ppm

Numeric, specify the mass error in ppm.

min_pkw

Numeric, specify the minimum peak width in seconds.

max_pkw

Numeric, specify the maximum peak width in seconds.

sn_thresh

Numeric, specify the signal to noise threshold.

mzdiff

Numeric, specify the minimum m/z difference for signals to be considered as different features when retention times are overlapping.

bw

Numeric, specify the band width (sd or half width at half maximum) of gaussian smoothing kernel to be applied during peak grouping.

min_frac

Numeric, specify fraction of samples in each group that contain the feature for it to be included.

min_sample_num

Numeric, specify minimum number of sample(s) in each group that contain the feature for it to be included.

max_feats

Numeric, specify the maximum number of features to be identified.

rt_filt

Boolean, if true, users must specify the minimum and maximum retention time to be included in the analysis. By default this is set to 200 - 1000.

rt_min

Numeric, specify the minimum retention time.

rt_max

Numeric, specify the maximum retention time.