LBMC » NucleoMiner

filter_for_coverage = FALSE ##<< Does it filter for plot coverage?

	if (only_f) {

		inputs = inputs[inputs[,1]==chr & inputs[,2] >= x_min - nuc_width & inputs[,3] == "F" & inputs[,2] <= x_max + nuc_width,]

	} else if (only_r) {

		inputs = inputs[inputs[,1]==chr & inputs[,2] >= x_min - nuc_width & inputs[,3] == "R" & inputs[,2] <= x_max + nuc_width,]			

	} else {

		inputs = inputs[inputs[,1]==chr & inputs[,2] >= x_min - nuc_width & inputs[,2] <= x_max + nuc_width,]

	}

    corrected_inputs_coords = inputs[,2] + nuc_width/2 * sign_from_strand(inputs[,3])

    inputs = inputs[inputs[,1]==chr & corrected_inputs_coords >= x_min & corrected_inputs_coords <= x_max,]    

	return(inputs)

# filter_tf_inputs = function(# Filter TemplateFilter inputs

# ### This function filters TemplateFilter inputs according genome area observed properties. It takes into account reads that are at the frontier of this area and the strand of these reads.

# inputs, ##<< TF inputs to be filtered.

# chr, ##<< Chromosome observed, here chr is an integer.

# x_min, ##<< Coordinate of the first bp observed.

# x_max, ##<< Coordinate of the last bp observed.

# nuc_width = 160, ##<< Nucleosome width.

# only_f = FALSE, ##<< Filter only F reads.

# only_r = FALSE, ##<< Filter only R reads.

# filter_for_coverage = FALSE, ##<< Does it filter for plot coverage?

# USE_DPLYR = FALSE ##<< Use dplyr lib to filter reads.

# ) {

#   n = names(inputs)

#

#   if (!USE_DPLYR) {

#     if (only_f) {

#       inputs_out = inputs[inputs[,1]==chr & inputs[,2] >= x_min - nuc_width & inputs[,3] == "F" & inputs[,2] <= x_max + nuc_width,]

#     } else if (only_r) {

#       inputs_out = inputs[inputs[,1]==chr & inputs[,2] >= x_min - nuc_width & inputs[,3] == "R" & inputs[,2] <= x_max + nuc_width,]

#     } else {

#       inputs_out = inputs[inputs[,1]==chr & inputs[,2] >= x_min - nuc_width & inputs[,2] <= x_max + nuc_width,]

#     }

#   } else {

#     names(inputs) = c("chr", "pos", "str", "lev")

#     if (only_f) {

#       inputs_out = filter(inputs, chr == chr,  pos >= x_min - nuc_width, str == "F", pos <= x_max + nuc_width)

#     } else if (only_r) {

#       inputs_out = filter(inputs, chr == chr, pos >= x_min - nuc_width, str == "R" & pos <= x_max + nuc_width)

#     } else {

#       inputs_out = filter(inputs, chr == chr, pos >= x_min - nuc_width, pos <= x_max + nuc_width)

#     }

#       # if (!filter_for_coverage) {

#       #   inputs$corrected_inputs_coords = inputs[,2] + nuc_width/2 * sign_from_strand(inputs[,3])

#       #   inputs = filter(inputs, chr == chr, corrected_inputs_coords >= x_min, corrected_inputs_coords <= x_max)

#       #   inputs$corrected_inputs_coords = NULL

#       # }

#   }

#

#   if (!filter_for_coverage) {

#     corrected_inputs_coords = inputs_out[,2] + nuc_width/2 * sign_from_strand(inputs_out[,3])

#     inputs_out = inputs_out[inputs_out[,1]==chr & corrected_inputs_coords >= x_min & corrected_inputs_coords <= x_max,]

#   }

#

#   names(inputs_out) = n

#   return(inputs_out)

# ### Returns filtred inputs.

# }