noise: Maximum Noise Estimation

In kylebario/concentr8r: MRS Data Preprocessing and Normalisation

Maximum Noise Estimation

Description

This function estimates the maximum level of noise for each spectra in an X matrix. The output of this function can be used as the noi variable in both pqNorm() and hmNorm()

Usage

noise(X_OG, ppm_OG, sh = c(9.5, 11), sd_mult = 5, method = "simple")

Arguments

X_OG	The numerical matrix containing the NMR data you wish to estimate the noise of. The rows must contain information of one whole spectrum and the columns contain the specific chemical shift variables.
ppm_OG	An array of chemical shift variables. ppm should be column matched to the X matrix you using.
sh	The concatenated ppm values that define the lower and upper bounds of the noise region. Default is c(9.5,11)
sd_mult	The value that the standard deviation will be multiplied by. Default = 5. This does not need to be changed.
method	Takes the strings 'simple' or 'topspin'. Defines what method is used to calculate the noise. Simple is the method detailed in details. Topspin is the method used by topspin which can be found in the help section of topspin.

Details

This function uses a combination of the functions mean and sd to find the standard deviation of the noise region as well as it's mean. The standard deviation is multiplied by five to capture any extreme outliers and added to the mean noise level to produce an estimation of maximum noise. The output of this function is intended for use in both the pqNorm() and hmNorm() functions so they can remove the noise from the spectra and produce clear results.

Value

This function returns an estimation of the maximum noise level for each spectra.

Author(s)

[e-mail]

See Also

Simple noise estimation methodology was adapted from histogram matching methods paper which can be found here: http://dx.doi.org/10.1007/s11306-018-1400-6

Other estimation: get_idx(), lw(), shift_pickr()

Examples

read_in(path = system.file('extdata',package='concentr8r'),
        exp_type = list(exp=c("PROF_URINE_NOESY")),
        n_spec = 'multiple')
noi <- noise(X, ppm, c(9.5,11))
cat(noi)

kylebario/concentr8r documentation built on Nov. 9, 2022, 12:47 a.m.